Method for identifying or characterizing properties of polymeric units

ABSTRACT

The invention relates to methods of identifying and characterizing properties of polymers to provide information about the polymer such as the charge of the polymer, the number and types or characteristics of units of the polymer and the sequence of the polymers. The invention also relates to methods of sequencing polymers such as nucleic acids, polypeptides and polysaccharides and methods for identifying a polysaccharide-protein interaction.

RELATED APPLICATION

This application us a continuation of U.S. application Ser. No.10/356,349, filed Jan. 31, 2003, allowed, which is a divisional of U.S.application Ser. No. 09/558,137, filed on Apr. 24, 2000, issued as U.S.Pat. No. 6,597,996, which claims priority under 35 U.S.C. §119 to U.S.Provisional Patent Application Nos. 60/130,747, filed Apr. 23, 1999,60/130,792, filed Apr. 23, 1999, 60/159,939, filed Oct. 14, 1999, and60/159,940, filed Oct. 14, 1999, the contents of each of which areincorporated herein by reference in their entirety.

BACKGROUND

Various notational systems have been used to encode classes of chemicalunits by assigning a unique code to each chemical unit in the class. Forexample, a conventional notational system for encoding amino acidsassigns a single letter of the alphabet to each known amino acid. Apolymer of chemical units may be represented using such a notationalsystem using a set of codes corresponding to the chemical units. Suchnotational systems have been used to encode polymers, such as proteins,in a computer-readable format. A polymer that has been represented insuch a computer-readable format according to a notational system may bestored and processed by a computer.

Conventional notational schemes for representing chemical units haverepresented the chemical units as characters (e.g., A, T, G, and C fornucleic acids), and have represented polymers of chemical units assequences or sets of characters. Various operations may be performed onsuch a notational representation of a chemical unit or a polymercomprised of chemical units. For example, a user may search a databaseof chemical units for a query sequence of chemical units. In such acase, the user typically provides a character-based notationalrepresentation of the sequence in the form of a sequence of characters,which is compared against the character-based notational representationsof sequences of chemical units stored in the database. Character-basedsearching algorithms, however, are typically slow because suchalgorithms search by comparing individual characters in the querysequence against individual characters in the sequences of chemicalunits stored in the database. The spread of such algorithms is thereforerelated to the length of the query sequence, resulting in particularlypoor performance for long query sequences.

The study of molecular and cellular biology is focused on themacroscopic structure of cells. We now know that cells have a complexmicrostructure that determine the functionality of the cell. Much of thediversity associated with cellular structure and function is due to theability of a cell to assemble various building blocks into diversechemical compounds. The cell accomplishes this task by assemblingpolymers from a limited set of building blocks referred to as monomers.The key to the diverse functionality of polymers is based in the primarysequence of the monomers within the polymer and is integral tounderstanding the basis for cellular function, such as why a celldifferentiates in a particular manner or how a cell will respond totreatment with a particular drug.

The ability to identify the structure of polymers by identifying theirsequence of monomers is integral to the understanding of each activecomponent and the role that component plays within a cell. Bydetermining the sequences of polymers it is possible to generateexpression maps, to determine what proteins are expressed, to understandwhere mutations occur in a disease state, and to determine whether apolysaccharide has better function or loses function when a particularmonomer is absent or mutated.

SUMMARY

Polymers may be characterized by identifying properties of the polymersand comparing those properties to reference polymers, a process referredto herein as property encoded nomenclature (PEN). In one embodiment, theproperties are encoded using a binary notation system, and thecomparison is accomplished by comparing the binary representations ofpolymers. For instance, in one aspect a sample polymer is subjected toan experimental constraint to modify the polymer, the modified polymeris compared to a reference database of polymers to identify a populationof polymers having a property that is the same as or similar to aproperty of the sample polymer. The method may be repeated until thepopulation of polymers in the reference database is reduced to one andthe identity of the sample polymer is known.

In a system including a database of properties of polymers of chemicalunits a method for determining the composition of a sample polymer ofchemical units having a known molecular weight and length is providedaccording to one aspect of the invention. The method includes the stepsof

-   -   (A) selecting, from the database, candidate polymers of chemical        units having the same length as the sample polymer of chemical        units and having molecular weights similar to the molecular        weight of the sample polymer of chemical units;    -   (B) performing an experiment on the sample polymer of chemical        units;    -   (C) measuring properties of the sample polymer of chemical units        resulting from the experiment; and    -   (D) eliminating, from the candidate polymers of chemical units,        polymers of chemical units having properties that do not        correspond to the experimental results.

In some embodiments the method also includes the step of:

-   -   (E) repeatedly performing the step (D) until the number of        candidate polymers of chemical units falls below a predetermined        threshold.

In other aspects the invention is a method for identifying a populationof polymers of chemical units having the same property as a samplepolymer of chemical units. The method includes the steps of determininga property of a sample polymer of chemical units, and comparing theproperty of the sample polymer to a reference database of polymers ofknown sequence and known properties to identify a population of polymersof chemical units having the same property as a sample polymer ofchemical units, wherein the reference database of polymers includesidentifiers corresponding to the chemical units of the polymers, each ofthe identifiers including a field storing a value corresponding to theproperty.

In one embodiment the step of determining a property of the samplepolymer involves the use of mass spectrometry, such as for example,matrix assisted laser desorption ionization mass spectrometry(MALDI-MS), electron spray-MS, fast atom bombardment mass spectrometry(FAB-MS) and collision-activated dissociation mass spectrometry (CAD) todetermine the molecular weight of the polymer. MALDI-MS, for instance,may be used to determine the molecular weight of the polymer with anaccuracy of approximately one Dalton.

The step of identifying a property of the polymer in other embodimentsmay involve the reduction in size of the polymer into pieces of severalunits in length that may be detected by strong ion exchangechromatography. The fragments of the polymer may be compared to thereference database polymers.

According to other aspects, the invention is a method for identifying asubpopulation of polymers having a property in common with a samplepolymer of chemical units. The method involves the steps of applying anexperimental constraint to the polymer to modify the polymer, detectinga property of the modified polymer, identifying a population of polymersof chemical units having the same molecular length as the samplepolymer, and identifying a subpopulation of the identified population ofpolymers having the same property as the modified polymer byeliminating, from the identified population of polymers, polymers havingproperties that do not correspond to the modified polymer. The steps maybe repeated on the modified polymer to identify a second subpopulationwithin the subpopulation of polymers having a second property in commonwith the twice modified polymer. Each of the steps may then be repeateduntil the number of polymers within the subpopulation falls below apredetermined threshold. The method may be performed to identify thesequence of the polymer. In this case the predetermined threshold ofpolymers within the subpopulation is two polymers.

In yet another aspect, the invention is a method for identifying asubpopulation of polymers having a property in common with a samplepolymer of chemical units. The method involves the steps of applying anexperimental constraint to the polymer to modify the polymer, detectinga first property of the modified polymer, identifying a population ofpolymers of chemical units having a second property in common with thesample polymer, and identifying a subpopulation of the identifiedpopulation of polymers having the same first property as the modifiedpolymer by eliminating, from the identified population of polymers,polymers having properties that do not correspond to the modifiedpolymer.

In one embodiment the experimental constraints applied to the polymerare different for each repetition. The experimental constrain may be anymanipulation which alters the polymer in such a manner that it will bepossible to derive structural information about the polymer or a unit ofthe polymer. In some embodiments the experimental constraint applied tothe polymer may be any one or more of the following constraints:enzymatic digestion, e.g., with an exoenzyme, an endoenzyme, arestriction endonuclease; chemical digestion; chemical modification;interaction with a binding compound; chemical peeling (i.e., removal ofa monosaccharide unit); and enzymatic modification, for instancesulfation at a particular position with a heparin sulfatesulfotransferases.

The property of the polymer that is detected by the method of theinvention may be any structural property of a polymer or unit. Forinstance the property of the polymer may be the molecular weight orlength of the polymer. In other embodiments the property may be thecompositional ratios of substituents or units, type of basic buildingblock of a polysaccharide, hydrophobicity, enzymatic sensitivity,hydrophilicity, secondary structure and conformation (i.e., position ofhelices), spatial distribution of substituents, ratio of one set ofmodifications to another set of modifications (i.e., relative amounts of2-O sulfation to N-sulfation or ratio of iduronic acid to glucuronicacid, and binding sites for proteins.

The properties of the modified polymer may be detected in any mannerpossible which depends on the property and polymer being analyzed. Inone embodiment the step of detection involves mass spectrometry such asmatrix assisted laser desorption ionization mass spectrometry(MALDI-MS), electron spray MS, fast atom bombardment mass spectrometry(FAB-MS) and collision-activated dissociation mass spectrometry (CAD).Alternatively, the step of detection involves strong ion exchangechromatography, for example, if the polymer has been digested intoseveral smaller fragments composed of several units each.

The method is based on a comparison of the sample polymer with apopulation of polymers of the same length or having at least oneproperty in common. In some embodiments the population of polymers ofchemical units includes every polymer sequence having the molecularweight of the sample polymer. In other embodiments the population ofpolymers of chemical units includes less than every polymer sequencehaving the molecular weight of the sample polymer. According to someembodiments the step of identifying includes selecting the population ofpolymers of chemical units from a database including molecular weightsof polymers of chemical units. Preferably the database includesidentifiers corresponding to chemical units of a plurality of polymers,each of the identifiers including a field storing a value correspondingto a property of the corresponding chemical unit.

According to another aspect of the invention a method for compositionalanalysis of a sample polymer is provided. The method includes the stepsof applying an experimental constraint to the sample polymer to modifythe sample polymer, detecting a property of the modified sample polymer,and comparing the modified sample polymer to a reference database ofpolymers of identical size as the polymer, wherein the polymers of thereference database have also been subjected to the same experimentalconstraint as the sample polymer, wherein the comparison provides acompositional analysis of the sample polymer.

In some embodiments the compositional analysis reveals the number andtype of units within the polymer. In other embodiments the compositionalanalysis reveals the identity of a sequence of chemical units of thepolymer.

Similarly to the aspects of the invention described above the propertiesof the polymer may be detected in any manner possible and will depend onthe particular property and polymer being analyzed. In one embodimentthe step of detection involves mass spectrometry such as matrix assistedlaser desorption ionization mass spectrometry (MALDI-MS), electron sprayMS, fast atom bombardment mass spectrometry (FAB-MS) andcollision-activated dissociation mass spectrometry (CAD). Preferably theexperimental constraint applied to the polymer is an enzymatic orchemical reaction which involves incomplete enzymatic digestion of thepolymer and wherein the steps of the method are repeated until thenumber of polymers within the reference database falls below apredetermined threshold. Alternatively, the step of detection involvescapillary electrophoresis, particularly when the experimental constraintapplied to the polymer involves complete degradation of the polymer intoindividual chemical units.

In one embodiment the reference database includes identifierscorresponding to chemical units of a plurality of polymers, each of theidentifiers including a field storing a value corresponding to aproperty of the corresponding chemical unit.

According to yet another aspect of the invention a method for sequencinga polymer is provided. The method includes the steps of applying anexperimental constraint to the polymer to modify the polymer, detectinga property of the modified polymer, identifying a population of polymershaving the same molecular length as the sample polymer and havingmolecular weights similar to the molecular weight of the sample polymer,identifying a subpopulation of the identified population of polymershaving the same property as the modified polymer by eliminating, fromthe identified population of polymers, polymers having properties thatdo not correspond to the modified polymer, and repeating the stepsapplying an experimental constraint, detecting a property andidentifying a subpopulation by applying additional experimentalconstraints to the polymer and identifying additional subpopulations ofpolymers until the number of polymers within the subpopulation is oneand the sequence of the polymer may be identified.

In another aspect the invention relates to a method for identifying apolysaccharide-protein interaction, by contacting a protein-coated MALDIsurface with a polysaccharide containing sample to produce apolysaccharide-protein-coated MALDI surface, removing unboundpolysaccharide from the polysaccharide-protein-coated MALDI surface, andperforming MALDI mass spectrometry to identify the polysaccharide thatspecifically interacts with the protein coated on the MALDI surface.

In one embodiment a MALDI matrix is added to thepolysaccharide-protein-coated MALDI surface. In other embodiments anexperimental constraint may be applied to the polysaccharide bound onthe polysaccharide-protein-coated MALDI surface before performing theMALDI mass spectrometry analysis. The experimental constraint applied tothe polymer in some embodiments is digestion with an exoenzyme ordigestion with an endoenzyme. In other embodiments the experimentalconstraint applied to the polymer is selected from the group consistingof restriction endonuclease digestion; chemical digestion; chemicalmodification; and enzymatic modification.

Each of the limitations of the invention can encompass variousembodiments of the invention. It is, therefore, anticipated that each ofthe limitations of the invention involving any one element orcombinations of elements may be included in each aspect of theinvention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a dataflow diagram of a system for sequencing a polymer.

FIG. 2 is a flow chart of a process for sequencing a polymer.

FIG. 3 is a flow chart of a process for sequencing a polymer using agenetic algorithm.

FIG. 4A-D is a set of diagrams depicting notation schemes for branchedchain analysis.

FIG. 5 is a mass line diagram.

FIG. 6 is a mass-line diagram for (A) Polysialic Acid with NAN and (B)Polysialic Acid with NGN.

FIG. 7 is a graph (A) depicting cleavage by Hep III of either G(●), I(◯)or I_(2S)(♦) linkages, and a graph (B) depicting same study as in A butwhere cleavage was performed with Hep I.

FIG. 8 is a graph depicting MALDI-MS analysis of the extended corestructures derived from enzymatic treatment of a mixture of bi- andtriantennary structures.

FIG. 9 is a graph depicting MALDI-MS analysis of the PSA polysaccharide.(A) intact polysaccharide structure. (B) Treatment of [A] with sialidasefrom A. urefaciens. (C) Digest of [B] with galactosidase from S.pneumoniae. (D) Digest of [C] with N-acetylhexosaminidase from S.pneumoniae. (E) Table of the analysis scheme with schematic structureand theoretical molecular masses. [◯]=mannose; [●]=fucose;[▪]=N-acetylglucosamine; [□]=galactose; and [Δ]=N-acetylneuraminic acid.Peaks marked with an asterisk are impurities, and the analyte peak isdetected both as M-H (m/z 2369.5) and as a monosodiated adduct (M+Na-2H,m/z 2392.6).

FIG. 10 is a graph depicting the results of enzymatic degradation of thesaccharide chain directly off of PSA. (A) PSA before the addition ofexoenzymes. (B) Treatment of (A) with sialidase results in a massdecrease of 287 Da, consistent with the loss of one sialic acid residue.(C) Treatment of (B) with galactosidase. (D) Upon digestion of (C) withhexosaminidase, a decrease of 393 Da indicates the loss of twoN-acetylglucosamine residues.

FIG. 11 is a graph depicting the results of treatment of biantennary andtriantennary saccharides with endoglycanse F2. (A) Treatment of thebiantennary saccharide results in a mass decrease of 348.6, indicatingcleavage between the GlcNAc residues. (B) Treatment of the triantennarysaccharide with the same substituents results in no cleavage showingthat EndoF2 primarily cleaves biantennary structures. (C) EndoF2treatment of heat denatured PSA. There is a mass reduction of 1709.7 Dain the molecular mass of PSA (compare B4C and B3a) indicating that thenormal glycan structure of PSA is biantennary.

DETAILED DESCRIPTION

The invention relates in some aspects to methods for characterizingpolymers to identify structural properties of the polymers, such as thecharge, the nature and number of units of the polymer, the nature andnumber of chemical substituents on the units, and the stereospecificityof the polymer. The structural properties of polymers may provide usefulinformation about the function of the polymer. For instance, theproperties of the polymer may reveal the entire sequence of units of thepolymer, which is useful for identifying the polymer. Similarly, if thesequence of the polymer was previously unknown, the structuralproperties of the polymer are useful for comparing the polymer to knownpolymers having known functions. The properties of the polymer may alsoreveal that a polymer has a net charge or has regions which are charged.This information is useful for identifying compounds that the polymermay interact with or predicting which regions of a polymer may beinvolved in a binding interaction or have a specific function.

Many methods have been described in the prior art for identifyingpolymers and in particular for identifying the sequence of units ofpolymers. Once the sequence of a polymer is identified the sequenceinformation is stored in a database and may be used to compare thepolymer with other sequenced polymers. Databases such as GENBANK enablethe storage and retrieval of information relating to the sequences ofnucleic acids which have been identified by researchers all over theworld. These databases typically store information using notationalsystems that encode classes of chemical units by assigning a unique codeto each chemical unit in the class. For example, a conventionalnotational system for encoding amino acids assigns a single letter ofthe alphabet to each known amino acid. Such databases represent apolymer of chemical units using a set of codes corresponding to thechemical units. Searches of such databases have typically been performedusing character-based comparison algorithms.

New methods for identifying structural properties of polymers which canutilize Bioinformatics and which differ from the prior art methods ofassigning a character to each unit of a polymer have been discovered.These methods are referred to as PEN (property encoded nomenclature). Inone aspect, the invention is based on the identification andcharacterization of properties of a polymer, rather than units of thepolymer, and the use of numeric identifiers to classify those propertiesand to facilitate information processing relating to the polymer.

The ability to identify properties of polymers and to manipulate theinformation concerning the properties of the polymer provide manyadvantages over prior art methods of characterizing polymers andBioinformatics. For instance, the methods of the invention may be usedto identify structural information and analyze complex polymers such aspolysaccharides which were previously very difficult to analyze usingprior art methods.

The heterogeneity and the high degree of variability of thepolysaccharide building blocks have hindered prior art attempts tosequence these complex molecules. With the advent of extremely sensitivetechniques like High Pressure Liquid Chromatography (HPLC), CapillaryElectrophoresis (CE) and Mass Spectrometry (MS) to isolate andcharacterize large biomolecules, significant advances have been made inisolating and purifying polysaccharide fragments containing specificsequences but extensive experimental manipulation is still required toidentify and sequence information. Additionally, in most of theseapproaches, plenty of information about the sequence is required inorder to design the experimental manipulations that will enable thesequencing of the polysaccharide. The methods of the prior art providesimple and rapid methods for identifying sequence information. Manyother advantages will be clear from the description of the preferredembodiments set forth below.

A “polymer” as used herein is a compound having a linear and/or branchedbackbone of chemical units which are secured together by linkages. Insome but not all cases the backbone of the polymer may be branched. Theterm “backbone” is given its usual meaning in the field of polymerchemistry. The polymers may be heterogeneous in backbone compositionthereby containing any possible combination of polymer units linkedtogether such as peptide-nucleic acids. In some embodiments the polymersare homogeneous in backbone composition and are, for example, a nucleicacid, a polypeptide, a polysaccharide, a carbohydrate, a polyurethane, apolycarbonate, a polyurea, a polyethyleneimine, a polyarylene sulfide, apolysiloxane, a polyimide, a polyacetate, a polyamide, a polyester, or apolythioester. A “polysaccharide” is a biopolymer comprised of linkedsaccharide or sugar units. A “nucleic acid” as used herein is abiopolymer comprised of nucleotides, such as deoxyribose nucleic acid(DNA) or ribose nucleic acid (RNA). A polypeptide as used herein is abiopolymer comprised of linked amino acids.

As used herein with respect to linked units of a polymer, “linked” or“linkage” means two entities are bound to one another by anyphysicochemical means. Any linkage known to those of ordinary skill inthe art, covalent or non-covalent, is embraced. Such linkages are wellknown to those of ordinary skill in the art. Natural linkages, which arethose ordinarily found in nature connecting the chemical units of aparticular polymer, are most common. Natural linkages include, forinstance, amide, ester and thioester linkages. The chemical units of apolymer analyzed by the methods of the invention may be linked, however,by synthetic or modified linkages. Polymers where the units are linkedby covalent bonds will be most common but also include hydrogen bonded,etc.

The polymer is made up of a plurality of chemical units. A “chemicalunit” as used herein is a building block or monomer which may be linkeddirectly or indirectly to other building blocks or monomers to form apolymer. The polymer preferably is a polymer of at least two differentlinked units. The particular type of unit will depend on the type ofpolymer. For instance DNA is a biopolymer comprised of a deoxyribosephosphate backbone composed of units of purines and pyrimidines such asadenine, cytosine, guanine, thymine, 5-methylcytosine, 2-aminopurine,2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, and othernaturally and non-naturally occurring nucleobases, substituted andunsubstituted aromatic moieties. RNA is a biopolymer comprised of aribose phosphate backbone composed of units of purines and pyrimidinessuch as those described for DNA but wherein uracil is substituted forthymidine. DNA units may be linked to the other units of the polymer bytheir 5′ or 3′ hydroxyl group thereby forming an ester linkage. RNAunits may be linked to the other units of the polymer by their 5′, 3′ or2′ hydroxyl group thereby forming an ester linkage. Alternatively, DNAor RNA units having a terminal 5′, 3′ or 2′ amino group may be linked tothe other units of the polymer by the amino group thereby forming anamide linkage.

Whenever a nucleic acid is represented by a sequence of letters it willbe understood that the nucleotides are in 5′→3′ order from left to rightand that “A” denotes adenosine, “C” denotes cytidine, “G” denotesguanosine, “T” denotes thymidine, and “U” denotes uracil unlessotherwise noted.

The chemical units of a polypeptide are amino acids, including the 20naturally occurring amino acids as well as modified amino acids. Aminoacids may exist as amides or free acids and are linked to the otherunits in the backbone of the polymers through their a-amino groupthereby forming an amide linkage to the polymer.

A polysaccharide is a polymer composed of monosaccharides linked to oneanother. In many polysaccharides the basic building block of thepolysaccharide is actually a disaccharide unit which may be repeating ornon-repeating. Thus, a unit when used with respect to a polysacchariderefers to a basic building block of a polysaccharide and may include amonomeric building block (monosaccharide) or a dimeric building block(disaccharide).

A “plurality of chemical units” is at least two units linked to oneanother.

The polymers may be native or naturally-occurring polymers which occurin nature or non-naturally occurring polymers which do not exist innature. The polymers typically include at least a portion of a naturallyoccurring polymer. The polymers may be isolated or synthesized de novo.For example, the polymers may be isolated from natural sources e.g.purified, as by cleavage and gel separation or may be synthesizede.g.,(i) amplified in vitro by, for example, polymerase chain reaction(PCR); (ii) synthesized by, for example, chemical synthesis; (iii)recombinantly produced by cloning, etc.

The invention is useful for identifying properties of polymers. A“property” as used herein is a characteristic (e.g., structuralcharacteristic) of the polymer that provides information (e.g.,structural information) about the polymer. When the term property isused with respect to any polymer except a polysaccharide the propertyprovides information other than the identity of a unit of the polymer orthe polymer itself. A compilation of several properties of a polymer mayprovide sufficient information to identify a chemical unit or even theentire polymer but the property of the polymer itself does not encompassthe chemical basis of the chemical unit or polymer.

When the term property is used with respect to polysaccharides, todefine a polysaccharide property, it has the same meaning as describedabove except that due to the complexity of the polysaccharide, aproperty may identify a type of monomeric building block of thepolysaccharide. Chemical units of polysaccharides are much more complexthan chemical units of other polymers, such as nucleic acids andpolypeptides. The polysaccharide unit has more variables in addition toits basic chemical structure than other chemical units. For example, thepolysaccharide may be acetylated or sulfated at several sites on thechemical unit, or it may be charged or uncharged. Thus, one property ofa polysaccharide may be the identity of one or more basic buildingblocks of the polysaccharides.

A basic building block alone, however, may not provide information aboutthe charge and the nature of substituents of the saccharide ordisaccharide. For example, a building block of uronic acid may beiduronic or glucuronic acid. Each of these building blocks may haveadditional substituents that add complexity to the structure of thechemical unit. A single property, however, may not identify suchadditional substitutes charges, etc., in addition to identifying acomplete building block of a polysaccharide. This information, however,may be assembled from several properties. Thus, a property of a polymeras used herein does not encompass an amino acid or nucleotide but doesencompass a saccharide or disaccharide building block of apolysaccharide.

The type of property that will provide structural information about apolymer will depend on the type of polymer being analyzed. For instance,if the polymer is a polysaccharide a property such as charge, molecularweight, nature and degree of sulfation or acetylation, or type ofsaccharide will provide structural information about the polymer. If thepolymer is a polypeptide then a property will provide information aboutcharge, acidity, etc. Properties include but are not limited to charge,chirality, nature of substituents, quantity of substituents, molecularweight, molecular length, compositional ratios of substituents or units,type of basic building block of a polysaccharide, hydrophobicity,enzymatic sensitivity, hydrophilicity, secondary structure andconformation (i.e., position of helices), spatial distribution ofsubstituents, ratio of one set of modifications to another set ofmodifications (i.e., relative amounts of 2-O sulfation to N-sulfation orratio of iduronic acid to glucuronic acid, and binding sites forproteins. Other properties will easily be identified by those ofordinary skill in the art. A substituent, as used herein is an atom orgroup of atoms that substitute a unit, but are not themselves the units.

The property of the polymer may be identified by any means known in theart. The procedure used to identify the property will depend on the typeof property. Molecular weight, for instance, may be determined byseveral methods including mass spectrometry. The use of massspectrometry for determining the molecular weight of polymers is wellknown in the art. Mass Spectrometry has been used as a powerful tool tocharacterize polymers because of its accuracy (±1 Dalton) in reportingthe masses of fragments generated e.g. by enzymatic cleavage and alsobecause only pM sample concentrations are required. For instancematrix-assisted laser desorption ionization mass spectrometry (MALDI-MS)has been described for identifying the molecular weight ofpolysaccharide fragments in publications such as Rhomberg, A. J. et al,PNAS, USA, v. 95, p. 4176-4181 (1998); Rhomberg, A. J. et al, PNAS, USA,v. 95, p. 12232-12237 (1998); and Ernst, S. et. al., PNAS, USA, v. 95,p. 4182-4187 (1998), each of which is hereby incorporated by reference.Other types of mass spectrometry known in the art, such as, electronspray-MS, fast atom bombardment mass spectrometry (FAB-MS) andcollision-activated dissociation mass spectrometry (CAD) may also beused to identify the molecular weight of the polymer or polymerfragments.

The mass spectrometry data may be a valuable tool to ascertaininformation about the polymer fragment sizes after the polymer hasundergone degradation with enzymes or chemicals. After a molecularweight of a polymer is identified, it may be compared to molecularweights of other known polymers. Because masses obtained from the massspectrometry data are accurate to one Dalton (1 D), a size of one ormore polymer fragments obtained by enzymatic digestion may be preciselydetermined, and a number of substituents (i.e., sulfates and acetategroups present) may be determined. One technique for comparing molecularweights is to generate a mass line and compare the molecular weight ofthe unknown polymer to the mass line to determine a subpopulation ofpolymers which have the same molecular weight. A “mass line” as usedherein is an information database, preferably in the form of a graph orchart which stores information for each possible type of polymer havinga unique sequence based on the molecular weight of the polymer. Thus, amass line may describe a number of polymers having a particularmolecular weight. A two-unit nucleic acid molecule (i.e., a nucleic acidhaving two chemical units) has 16 (4 units²) possible polymers at amolecular weight corresponding to two nucleotides. A two-unitpolysaccharide (i.e., disaccharide) has 32 possible polymers at amolecular weight corresponding to two saccharides. Thus, a mass line maybe generated by uniquely assigning a particular mass to a particularlength of a given fragment (all possible di, tetra, hexa, octa, up to ahexadecasaccharide), and tabulating the results (An Example is shown inFIG. 5).

Table 1 below shows an example of a computed set of values for apolysaccharide. From Table 1, a number of chemical units of a polymermay be determined from the minimum difference in mass between a fragmentof length n+1 and a fragment of length n. For example, if the repeat isa disaccharide unit, a fragment of length n has 2n monosaccharide units.For example, n=1 may correspond to a length of a disaccharide and n=2may correspond to a length of a tetrasaccharide, etc. TABLE 1 Minimumdifference in mass Fragment Length n between n + 1 and n(D (Dalton)) 1101.13 2 13.03 3 13.03 4 9.01 5 9.01 6 4.99 7 4.99 8 0.97 9 0.97

Because mass spectrometry data indicates the mass of a fragment to 1 Daccuracy, a length may be assigned uniquely to fragment by looking up amass on the mass line. Further, it may be determined from the mass linethat, within a fragment of particular length higher than a disaccharide,there is a minimum of 4.02 D different in masses indicating that twoacetate groups (84.08 D) replaced a sulfate group (80.06 D). Therefore,a number of sulfates and acetates of a polymer fragment may bedetermined from the mass from the mass spectrometry data and, suchnumber may be assigned to the polymer fragment.

In addition to molecular weight, other properties may be determinedusing methods known in the art. The compositional ratios of substituentsor chemical units (quantity and type of total substituents or chemicalunits) may be determined using methodology known in the art, such ascapillary electrophoresis. A polymer may be subjected to an experimentalconstraint such as enzymatic or chemical degradation to separate each ofthe chemical units of the polymers. These units then may be separatedusing capillary electrophoresis to determine the quantity and type ofsubstituents or chemical units present in the polymer. Additionally, anumber of substituents or chemical units can be determined usingcalculations based on the molecular weight of the polymer.

In the method of capillary gel-electrophoresis, reaction samples may beanalyzed by small-diameter, gel-filled capillaries. The small diameterof the capillaries (50 μm) allows for efficient dissipation of heatgenerated during electrophoresis. Thus, high field strengths can be usedwithout excessive Joule heating (400 V/m), lowering the separation timeto about 20 minutes per reaction run, therefor increasing resolutionover conventional gel electrophoresis. Additionally, many capillariesmay be analyzed in parallel, allowing amplification of generated polymerinformation.

In addition to being useful for identifying a property, compositionalanalysis also may be used to determine a presence and composition of animpurity as well as a main property of the polymer. Such determinationsmay be accomplished if the impurity does not contain an identicalcomposition as the polymer. To determine whether an impurity is presentmay involve accurately integrating an area under each peak that appearsin the electrophoretogram and normalizing the peaks to the smallest ofthe major peaks. The sum of the normalized peaks should be equal to oneor close to being equal to one. If it is not, then one or moreimpurities are present. Impurities even may be detected in unknownsamples if at least one of the disaccharide units of the impuritydiffers from any disaccharide unit of the unknown.

If an impurity is present, one or more aspects of a composition of thecomponents may be determined using capillary electrophoresis. Becauseall known disaccharide units may be baseline-separated by the capillaryelectrophoresis method described above and because migration timestypically are determined using electrophoresis (i.e., as opposed toelectroosmotic flow) and are reproducible, reliable assignment to apolymer fragment of the various saccharide units may be achieved.Consequently, both a composition of the major peak and a composition ofa minor contaminant may be assigned to a polymer fragment. Thecomposition for both the major and minor components of a solution may beassigned as described below.

One example of such assignment of compositions involves determining thecomposition of the major AT-III binding HLGAG decasaccharide (+DDD4-7)and its minor contaminant (+D5D4-7) present in solution in a 9:1 ratio.Complete digestion of this 9:1 mixture with a heparinases yields 4peaks: three representative of the major decasaccharide (viz., D, 4, and−7) which are also present in the contaminant and one peak, 5, that ispresent only in the contaminant. In other words, the area of each peakfor D, 4, and −7 represents an additive combination of a contributionfrom the major decasaccharide and the contribution from the contaminant,whereas the peak for 5 represents only the contaminant.

To assign the composition of the contaminant and the major component,the area under the 5 peak may be used as a starting point. This arearepresents an area under the peak for one disaccharide unit of thecontaminant. Subtracting this area from the total area of 4 and −7 andsubtracted twice this area from an area under D yields a 1:1:3 ratio of4:−7:D. Such a ratio confirms the composition of the major component andindicates that the composition of the impurity is two Ds, one 4, one −7and one 5.

Methods of identifying other types of properties may be easilyidentifiable to those of skill in the art and may depend on the type ofproperty and the type of polymer. For example, hydrophobicity may bedetermined using reverse-phase high-pressure liquid chromatography(RP-HPLC). Enzymatic sensitivity may be identified by exposing thepolymer to an enzyme and determining a number of fragments present aftersuch exposure. The chirality may be determined using circular dichroism.Protein binding sites may be determined by mass spectrometry, isothermalcalorimetry and NMR. Enzymatic modification (not degradation) may bedetermined in a similar manner as enzymatic degradation, i.e., byexposing a substrate to the enzyme and using MALDI-MS to determine ifthe substrate is modified. For example, a sulfotransferase may transfera sulfate group to an HS chain having a concomitant increase in 80 Da.Conformation may be determined by modeling and nuclear magneticresonance (NMR). The relative amounts of sulfation may be determined bycompositional analysis or approximately determined by Ramanspectroscopy.

In some aspects the invention is useful for generating, searching andmanipulating information about polymers. In this aspect the completebuilding block of a polymer is assigned a unique numeric identifier,which may be used to classify the complete building block. For instanceif a polysaccharide is being analyzed, each numeric identifier wouldrepresent a complete building block of a polysaccharide, including theexact chemical structure as defined by the basic building block of apolysaccharide and all of its substituents, charges etc. A basicbuilding block refers to a basic structure of the polymer unit e.g., abasic ring structure of a polysaccharide, such as iduronic acid orglucuronic acid but does not include substituents, charges etc. Theinformation is generated and processed in the same manner as describedabove with respect to “properties” of polymers.

Currently, saccharide fragments are detected in capillaryelectrophoresis by monitoring at 232 nm, the wavelength at which theΔ^(4,5) double bond, generated upon heparinase cleavage, absorbs.However, other detection methods are possible. First, nitrous acidcleavage of heparin fragments, followed by reduction with ³H-sodiumborohydride yields degraded fragments having a ³H radioactive tag. Thisrepresents both a tag which may be followed by capillary electrophoresis(counting radioactivity) or mass spectrometry (by the increase in mass).Another method of using radioactivity would be to label the heparinfragment with S³⁵. Similar to the types of detection possible for³H-labeled fragments, S³⁵ labeled fragments may be useful forradioactive detection (CE) or measurement of mass differences (MS).

Especially in the case of S³⁵, this detection will be powerful. In thiscase, the human sulfotransferases may be used to label specifically acertain residue. This will give additional structural information.

Nitrous acid degraded fragments, unlike heparinase-derived fragments, donot have a UV-absorbing chromophore. As we have shown, MALDI-MS willrecord the mass of heparin fragments regardless of how they are derived.For CE, two methods may be used to monitor fragments that lack asuitable chromophore. First is indirect detection of fragments. We maydetect heparin fragments with our CE methodology using a suitablebackground absorber, e.g., 1,5-napthalenedisulfonic acid. The secondmethod for detection involves chelation of metal ions by saccharides.The saccharide-metal complexes may be detected using UV-Vis just likemonitoring the unsaturated double bond.

Other groups have begun the process of raising antibodies to specificHLGAG sequences. We have previously shown that proteins, e.g.,angiogenin, FGF, may be used as the complexing agent instead of asynthetic, basic peptide. By extension, antibodies could be used as acomplexing agent for MALDI-MS analysis. This enables us to determinewhether specific sequences are present in an unknown sample simply byobserving whether a given antibody with a given sequence specificitycomplexes with the unknown using MALDI-MS.

The final point is that using mass tags, we may distinguish the reducingend of a glycosaminoglycan from the non-reducing end. All of these tagsinvolve selective chemistry with the anomeric OH (present at thereducing end of the polymer), thus labeling occurs at the reducing endof the chain. One common tag is 2-aminobenzoic acid which isfluorescent. In general tags involve chemistry of the following types:(1) reaction of amines with the anomeric position to form imines (i.e.,2-aminobenzoic acid), hydrazine reaction to form hydrazones, andreaction of semicarbazones with the anomeric OH to form semicarbazides.Commonly used tags (other than 2-aminobenzoic acid) include thefollowing compounds:

-   1. semicarbazide-   2. Girard's P reagent-   3. Girard's T reagent-   4. p-aminobenzoic ethyl ester-   5. biotin-x-hydrazide-   6. 2-aminobenzamide-   7. 2-aminopyridine-   8. anthranilic acid-   9. 5-[(4,6-dichlorotriazine-2-yl)amino]-fluorescein-   10. 8-aminonaphthalene-1,3,6-trisulfonic acid-   11. 2-aminoacridone

Referring to FIG. 1, a system 100 for sequencing polymers is shown. Thesystem 100 includes a polymer database 102 which includes a plurality ofrecords storing information corresponding to a plurality of polymers.Each of the records may store information about properties of thecorresponding polymer, properties of the corresponding polymer'sconstituent chemical units, or both. The polymers for which informationis stored in the polymer database 102 may be any kind of polymers. Forexample, the polymers may include polysaccharides, nucleic acids, orpolypeptides. In one embodiment, each of the records in the polymerdatabase 102 includes a polymer identifier (ID) that identifies thepolymer corresponding to the record. The record also includes chemicalunit identifiers (IDs) corresponding to chemical units that areconstituents of the polymer corresponding to the record. Polymers may berepresented in the polymer database in other ways. For example, recordsin the polymer database 102 may include only a polymer ID or may onlyinclude chemical unit IDs.

The polymer database 102 may be any kind of storage medium capable ofstoring information about polymers as described herein. For example, thepolymer database 102 may be a flat file, a relational database, a tablein a database, an object or structure in a computer-readable volatile ornon-volatile memory, or any data accessible to a computer program, suchas data stored in a resource fork of an application program file on acomputer-readable storage medium.

In one embodiment, a polymer ID includes a plurality of fields forstoring information about properties of the polymer corresponding to therecord containing the polymer ID. Similarly, in one embodiment, chemicalunit IDs include a plurality of fields for storing information aboutproperties of the chemical unit corresponding to the chemical unit ID.Although the following description refers to the fields of chemical unitIds, such description is equally applicable to the fields of polymerIDs.

The fields of chemical unit IDs may store any kind of value that iscapable of being stored in a computer readable medium, such as a binaryvalue, a hexadecimal value, an integral decimal value, or a floatingpoint value. The fields may store information about any properties ofthe corresponding chemical unit.

A compositional analyzer 108 receives as input a sample polymer 106 andgenerates as output polymer composition data 110 that is descriptive ofthe composition of the sample polymer. A compositional analyzer as usedherein is any type of equipment or experimental procedure that may beused to identify a property of a polymer modified by an experimentconstraint, such as those described above. These include, for instance,but are not limited to capillary electrophoresis, mass spectrometry, andchromatography. The polymer composition data 110 includes informationabout the sample polymer 106, such as the properties of the chemicalunits in the sample polymer 106 and the number of chemical units in thesample polymer 106. A sequencer 112 generates a candidate list 116 of asubpopulation of polymers that might match the sample polymer 106 in theprocess of sequencing the sample polymer 106 using information containedin a mass line 114 and the polymer database 102. A candidate list isalso referred to herein as a “population” of polymers. At the end of thesequencing process, the candidate list 116 contains zero or morepolymers that correspond to the sample polymer 106. A subpopulation ofpolymers is defined as a set of polymers having at least two propertiesin common with a sample polymer. It is useful to identify subpopulationsof polymers in order to have an information set with which to comparethe sample polymer 106.

Consider, for example, the sequence DD7DAD-7, which is atetradecasaccharide (14 mer) of HLGAG containing 20 sulfate groups. Thecompositional analyzer 108 may, for example, perform compositionalanalysis of DD7DAD-7 by degrading the sequence to its disaccharidebuilding blocks and analyzing the relative abundance of each unit usingcapillary electrophoresis to generate the polymer composition data 110.The polymer composition data 110 in this case would show a major peakcorresponding to ±D, a peak about ½ the size of the major peakcorresponding to ±7 and another peak about ¼ the size of the major peakcorresponding to ±A. Note that the ± sign is used because degradation byheparinase would create a double bond between the C4 and C5 atoms in theuronic acid ring thereby leading to the loss of the iduronic vs.glucuronic acid information. From the polymer composition data 110, itmay be inferred that there are 4±Ds, 2±7s and a ±A in the sequence.

Referring to FIG. 2, a process 200 that may be performed by thesequencer 112 to sequence the sample polymer 106 is shown. The sequencer112 receives the polymer composition data 110 from the compositionalanalyzer 108. The sequencer 112 uses the polymer composition data 110and the information contained in the polymer database 102 to generate aninitial candidate list 116 of all possible polymers: (1) having the samelength as the sample polymer 106 and (2) having the same constituentchemical units as the sample polymer 106 (step 204).

For example, consider the sequence DD7DAD-7 mentioned above. The polymercomposition data 110 indicates that the sequence includes 4±Ds, 2±7s andone ±A, and indicates that the length of the sample polymer 106 isseven. In this case, step 204 (generation of the candidate list 116)involves generating all possible sequences having the same length as thesample polymer 106 and having 4±Ds, 2±7s and a ±A. In one embodiment,the sequencer 112 uses a brute force method to generate all sequenceshaving these characteristics by generating all sequences of length sevenhaving 4±Ds, 2±7s and a ±A using standard combinatoric methods.

The sequencer 112 then uses the data from the mass line 114 toprogressively eliminate sequences from the list generated in step 204until the number of sequences in the list reaches a predeterminedthreshold (e.g., one). To perform such elimination, in one embodiment,the sequencer 112 calculates the value of a predetermined property ofeach of the polymers in the candidate list 116 (step 206). Thepredetermined property may, for example, be the mass of the polymer. Anexample method for calculating the mass of a polymer will be describedin more detail below. The sequencer 112 compares the calculated valuesof the predetermined property of the polymers in the candidate list 116to the value of the predetermined property of the sample polymer 106(step 208). The sequencer 112 eliminates candidate polymers from thecandidate list 116 whose predetermined property values do not match thevalue of the predetermined property of the sample polymer 106 within apredetermined range (step 208). For example, if the predeterminedproperty is molecular weight, the predetermined range may be ±1.5 D.

The sequencer 112 applies an experimental constraint to the samplepolymer 106 to modify the sample polymer 106 (step 210). An“experimental constraint” as used herein is a biochemical processperformed on a polymer which results in modification to the polymerwhich may be detected. Experimental constraints include but are notlimited to enzymatic digestion, e.g., with an exoenzyme, an endoenzyme,a restriction endonuclease; chemical digestion; chemical modification;interaction with a binding compound; chemical peeling (i.e., removal ofa monosaccharide unit); and enzymatic modification, for instancesulfation at a particular position with a heparan sulfatesulfotransferases.

The sequencer 112 measures properties of the modified sample polymer 106(step 212). The sequencer 112 eliminates from the candidate list 116those candidate polymers having property values that do not match theproperty values of the experimental results 122 (step 214).

If the size of the candidate list 116 is less than a predeterminedthreshold (e.g., 1) (step 216), then the sequencer 112 is done (step218). The contents of the candidate list 116 at this time represent theresults of the sequencing process. The candidate list 116 may containzero or more polymers, depending upon the contents of the polymerdatabase 102 and the value of the predetermined threshold. If the sizeof the candidate list 116 is not less than the predetermined threshold(step 216), steps 210-216 are repeated until the size of the candidatelist 116 falls below the predetermined threshold. When the sequencer 112is done (step 218), the sequencer 112 may, for example, display thecandidate list 116 to the user on an output device such as a computermonitor.

Referring to FIG. 3, in another embodiment, the sequencer 112 uses agenetic algorithm process 300 to generate the initial candidate list 116and to modify the candidate list 116 in order to arrive at a finalcandidate polymer that identifies the sequence of the sample polymer106. The sequencer 112 generates a population of random sequences withthe composition indicated by the polymer composition data 110 and havingthe same length as the sample polymer 106 (step 302). The sequencer 112evaluates the fitness (score) of the polymers in the candidate list 116using a scoring function based on the enzymatic degradation of enzymeENZ (step 304). The genetic algorithm process 300 uses the fitnessvalues to decide which of the sequences in the candidate list 116 cansurvive into the next generation and which of the sequences in thecandidate list 116 has the highest chance of producing other sequencesof equal or higher fitness by cross-over and mutation. The sequencer 112then performs cross-over and mutation operations that select for fitsequences in the candidate list 116 into the next generation (step 306).If at least a predetermined number (e.g., three) of generations of thecandidate list 116 include copies of the correct sequence with themaximum fitness (step 308), then the sequencer 112 is done sequencing.Otherwise, the sequencer 112 repeats steps 304-306 until the conditionof step 308 is satisfied. Cross-over and mutation operations are used bygenetic algorithms to randomly sample the different regions of a searchspace.

In one embodiment, steps 210 and 212 are automated (e.g., carried out bya computer). For example, after the initial candidate list 116 has beengenerated (step 208), the sequencer 112 may divide the candidate list116 into categories (the categories are preferably based on properties),such as hepI cleavable, hepIII cleavable, and nitrous acid cleavable(the property is enzymatic sensitivity). The sequencer 112 may thensimulate the corresponding degradation or modification of the sequencespresent in each of the categories and search for those sequences thatgive fragments of unique masses. Based on the population of sequencesthat can give fragments of unique masses upon degradation ormodification, the sequencer 112 chooses the particular enzyme orchemical as the experimental constraint to eliminate candidate polymersfrom the candidate list 116 (step x). Although in this example onlyhepI, hepIII, and nitrous acid are used, other experimental constraintssuch as enzymes may be used including the exoenzymes and other HLGAGdegrading chemicals.

In another embodiment, the sequencer 112 uses a chemical characteristicto guide the choice of experimental constraint. For example, normalizedfrequencies of chemical units of known polymers containing I_(2S), G,H_(NS), and H_(Nac) may be calculated. For example, the normalizedfrequency f(I_(2S)) of chemical units containing I_(2S) may becalculated as f(I_(2S))=(number of disaccharide units containingI_(2S))/(number of disaccharide units). An example set of normalizedfrequencies calculated for known sequences in this way is shown in table2 below. TABLE 2 Constraints used for Sequence f(I_(2S)) f(G) f(H_(N)S)f(H_(NAc)) convergence Octa2 DDD-5 0.75 0.25 1 0 Hep I and Hep IIIdegradation FGF binding 1 0 1 0 Hep I normal and DDDDD exhaustivedegradation ATIII binding 0.6 0.2 0.8 0.2 Hep I, Hep II and DDD4-7nitrous acid degradation

The “constraints used for convergence” column indicates constraints thathave been shown empirically to achieve convergence for the correspondingknown sequence. Once compositional analysis has been performed on asample (unknown) polymer, the relative frequencies of I_(2S), G, H_(NS),and H_(NAc) in the sample sequence may be compared to the relativefrequencies of the known sequences using the table above. To select aset of experimental constraints to apply to the sample polymer, therelative frequencies of the sample polymer may be compared to therelative frequencies of the known sequences in the table above. A knownsequence with relative frequencies that are similar to the relativefrequencies of the sample polymer may then be selected, and theexperimental constraints identified with the selected sequence (as shownin the table) may then be applied to the, sample polymer.

For example, Table 2 demonstrates that the presence of f(G) andf(H_(NAc)) are important factors in the decision to use hepIII andnitrous acid, because nitrous acid clips after a H_(NS), and hepIIIclips after a disaccharide unit containing G. The disaccharide unitI_(2S)—H_(NS,6)S is the dominant unit in heparin-like regions (i.e.,highly-sulfated regions) of the HLGAG chains. Therefore, if a sequenceis more heparin-like, then hepI may be chosen as the default enzyme andthe information content present in chemical units containing G andH_(NAc) become important for choosing enzymes and chemicals other thanhepI. Similarly, for low-sulfated regions on HLGAG chains, hepIII may bea default enzyme and f(I_(2S)) and f(H_(NS)) become important forchoosing hepI and nitrous acid. Similarly, one may also calculate thepositional sulfate or acetate distribution along the chain and generatethe criterion for using the sulfotransferases or sulfateases forconvergence.

In one embodiment, the polymer database 102 stores the mass of eachpolymer in the polymer database 102. In this embodiment, step 206(described above) may be performed merely by retrieving the mass of thecorresponding polymer from the polymer database 102. In anotherembodiment, the polymer database 102 includes information indicating amass of a baseline polymer. For example, in one embodiment the polymerdatabase 102 stores information about disaccharides: Referring to Table3, which illustrates one use of a binary notational representationsystem to notate disaccharides, it may be seen that the mass of theI—H_(NAc) disaccharide unit is 379.33 D. TABLE 3 ALPH MASS I/G 2X 6X 3XNX CODE DISACC (ΔU) 0 0 0 0 0 0 I-H_(NAc) 379.33 0 0 0 0 1 1 I-H_(NS)417.35 0 0 0 1 0 2 I-H_(NAc, 3S) 459.39 0 0 0 1 1 3 I-H_(NS, 3S) 497.410 0 1 0 0 4 I-H_(NAc, 6S) 459.39 0 0 1 0 1 5 I-H_(NS, 6S) 497.41 0 0 1 10 6 I- 539.45 H_(NAc, 3S, 6S) 0 0 1 1 1 7 I- 577.47 H_(NS, 3S, 6S) 0 1 00 0 8 I_(2S)-H_(NAc) 459.39 0 1 0 0 1 9 I_(2S)-H_(NS) 497.41 0 1 0 1 0 AI_(2S)- 539.45 H_(NAc, 3S) 0 1 0 1 1 B I_(2S)-H_(NS, 3S) 577.47 0 1 1 00 C I_(2S)- 539.45 H_(NAc, 6S) 0 1 1 0 1 D I_(2S)-H_(NS, 6S) 577.47 0 11 1 0 E I_(2S)- 619.51 H_(NAc, 3S, 6S) 0 1 1 1 1 F I_(2S)- 657.53H_(NS, 3S, 6S) 1 0 0 0 0 −0 G-H_(NAc) 379.33 1 0 0 0 1 −1 G-H_(NS)417.35 1 0 0 1 0 −2 G-H_(NAc, 3S) 459.39 1 0 0 1 1 −3 G-H_(NS, 3S)497.41 1 0 1 0 0 −4 G-H_(NAc, 6S) 459.39 1 0 1 0 1 −5 G-H_(NS, 6S)497.41 1 0 1 1 0 −6 G- 539.45 H_(NAc, 3S, 6S) 1 0 1 1 1 −7 G- 577.47H_(NS, 3S, 6S) 1 1 0 0 0 −8 G_(2S)-H_(NAc) 459.39 1 1 0 0 1 −9G_(2S)-H_(NS) 497.41 1 1 0 1 0 −A G_(2S-) 539.45 H_(NAc, 3S) 1 1 0 1 1−B G_(2S)-H_(NS, 3S) 577.47 1 1 1 0 0 G_(2S)- H_(NAc, 6S) 1 1 1 0 1 −DG_(2S)-H_(NS, 6S) 577.47 1 1 1 1 0 −E G_(2S)- 619.51 H_(NAc, 3S, 6S) 1 11 1 1 −F G_(2S)- 657.53 H_(NS, 3S, 6S)

In addition to the hexadecimal codes used in table 1 the following extrasymbols were used to represent modifications in the disaccharidebuilding block: 5-membered anhydromannitol ring—′; uronic acid with aC4—C5 unsaturated linkage—±; reducing end disaccharide unit with a masstag—(superscript) t; disaccharide unit without the uronic acid—*. Thepolymer database 102 may include information indicating that sulfationat a position of a polymer contributes 80.06 D to the mass of thepolymer and that substitution of a sulfate for an acetate contributes anadditional 38.02 D to the mass of the polymer. Therefore, the mass M ofany polymer in the polymer database 102 may be calculated using thefollowing formula:M=379.33+[0 80.06 80.06 80.06 38.02]*C,where C is the vector containing the binary representation of thepolymer and * is a vector multiplication operator. For example, the massof the disaccharide unit I_(2S)—H_(NS,6S), having a binaryrepresentation of 01101, would be equal to 379.33+[0 80.06 80.06 80.0638.02]* [01101]=379.33+0+80.06*1+80.06*1+80.06*0+38.02*1=577.47D.

Although the invention encompasses all polymers, the use of the,invention is described in more detail with respect to polysaccharidesbecause of the complex nature of polysaccharides. The invention,however, is not limited to polysaccharides. The heterogeneity of theheparin-like-glycosaminoglycan (HLGAG) fragments and the high degree ofvariability in their saccharide building blocks have hindered theattempts to sequence these complex molecules.Heparin-like-glycosaminoglycans (HLGAGs) which include heparin andheparan sulfate are complex polysaccharide molecules made up ofdisaccharide repeat units of hexoseamine and glucuronic/iduronic acidthat are linked by α/β 1-4 glycosidic linkages. These defining units maybe modified by sulfation at the N, 3-O and 6-O position of thehexoseamine, 2-O sulfation of the uronic acid and C5 epimerization thatconverts the glucuronic acid to iduronic acid. Schematically thedisaccharide unit of HLGAG may be represented as(α1→4)I/G_(2OX)(α/β1→4)H_(3OX,NY) ^(6OX)(α1→4)where

X may be sulfated (—SO3H) or unsulfated (—H)

Y may be sulfated (—SO3H) or acetylated (—COCH3)

HLGAGs may be represented using a notational system in which an HLGAG isrepresented by a polymer ID (described above). The fields of the polymerID may store any kinds of values, such as single-bit values,single-digit hexadecimal values, or decimal values. In one embodiment,the polymer ID representing an HLGAG includes each of the followingfields: (1) a field for storing a value indicating whether the polymercontains an iduronic or a glucuronic acid (I/G); (2) a field for storinga value indicating whether the 2X position of the iduronic or glucuronicacid is sulfated or unsulfated; (3) a field for storing a valueindicating whether the hexoseamine is sulfated or unsulfated; (4) afield indicating whether the 3X position of the hexoseamine is sulfatedor unsulfated; and (5) a field indicating whether the NX position of thehexoseamine is sulfated or acetylated.

In one embodiment, each of the fields is represented as a single bit. Anexample of the use of this scheme to encode HLGAGs is shown in Table 1.Bit values for each of the fields may be assigned in any manner. Forexample, with respect to the I/G field, in one embodiment a value of oneindicates Iduronic and a value of zero indicates Glucuronic, while inanother embodiment a value of one indicates Glucuronic and a value ofzero indicates Iduronic.

In one embodiment, the four fields (2X, 6X, 3X, and NX) is representedas a single hexadecimal (base 16) number where each of the four fieldsrepresents one of the bits of the hexadecimal number. Using hexadecimalnumbers to represent disaccharide units is convenient both forrepresentation and processing because hexadecimal digits are a commonform of representation used by conventional computers. In a furtherembodiment, the five fields (I/G, 2X, 6X, 3X, NX) are represented as asigned hexadecimal digit, in which the four fields (2X, 6X, 3X, NX) areused to code a single-digit hexadecimal number as described above andthe I/G field is used as a sign bit. In this embodiment, the hexadecimalnumbers 0-F may be used to code units containing iduronic acid and thehexadecimal numbers −0 to −F may be used to code units containingglucuronic acid. The polymer unit ID may, however, be encoded in otherways, such as by using a twos-complement representation.

HLGAG fragments may be degraded using enzymes such as heparin lyaseenzymes or nitrous acid and they may also be modified using differentenzymes that transfer sulfate groups to the positions mentioned earlieror remove the sulfate groups from those positions. The modifying enzymesare exolytic and non-processive which means that they just act once onthe non reducing end and will let go of the heparin chain withoutsequentially modifying the rest of the chain. For each of the modifiablepositions in the disaccharide unit there exits a modifying enzyme. Anenzyme that adds a sulfate group is called a sulfotransferase and anenzyme that removes a sulfate group is called a sulfatase. The modifyingenzymes include 2-O sulfatase/sulfotransferase, 3-Osulfatase/sulfotransferase, 6-O sulfatase/sulfotransferase andN-deacetylase-N-sulfotransferase. The function of these enzymes isevident from their names, for example a 2-O sulfotransferase transfers asulfate group to the 2-O position of an iduronic acid (2-O sulfatedglucuronic acid is a rare occurrence in the HLGAG chains) and a 2-Osulfatase removes the sulfate group from the 2-O position of an iduronicacid.

HLGAG degrading enzymes include heparinase-I, heparinase-II,heparinase-III, D-glucuronidase and L-iduronidase. The heparinasescleave at the glycosidic linkage before a uronic acid. Heparinase Iclips at a glycosidic linkage before a 2-O sulfated iduronic acid.Heparinase-III cleaves at a glycosidic linkage before an unsulfatedglucuronic acid. Heparinase-II cleaves at both Hep-I and Hep-IIIcleavable sites. After cleavage by the heparinases the uronic acidbefore which the cleavage occurs loses the information of iduronic vs.glucuronic acid because a double bond is created between the C4 and C5atoms of the uronic acid.

Glucuronidase and iduronidase, as their name suggests cleave at theglycosidic linkage after a glucuronic acid and iduronic acidrespectively. Nitrous acid clips randomly at glycosidic linkages after aN-sulfated hexosamine and converts the six membered hexosamine ring to a5 membered anhydromannitol ring.

The above rules for the enzymes may easily be encoded into a computer asdescribed above using binary arithmetic so that the activity of anenzyme on a sequence may be carried out using simple binary operators togive the fragments that would be formed from the enzymatic activity.

These techniques may be used to construct a database of polysaccharidesequences. In some aspects the invention is a database of polysaccharidesequences, as well as, motif search and sequence alignment algorithmsfor obtaining valuable information about the nature ofpolysaccharide-protein interactions that are vital for the biologicalfunctioning of these molecules. The sequence information in the databaseof polysaccharide sequences may also be used to provide valuable insightinto sequence-structure relationships of these molecules.

In addition to the use of the methods of the invention for sequencingpolymers, the methods may be used for any purpose in which it isdesirable to identify structural properties related to a polymer. Forinstance the methods of the invention may be used for analysis of lowmolecular weight heparin. By limited digestion of LMWH and analysis byCE and MALDI-MS, we may obtain an “digest spectrum” of variouspreparations of LMWH, thus deriving information about the compositionand variations thereof. Such information is of value in terms of qualitycontrol for LMWH preparations.

The methods are also useful for understanding the role of HLGAGs infundamental biological processes. Already MS has been used to look atthe presence of various proteins as a function of time in Drosophiladevelopment. In a similar fashion HLGAG expression can be as a functionboth of position and of time in Drosophila development. Similarly themethods may be used as a diagnostic tool for human diseases. There is agroup of human diseases called mucopolysaccharidosis (MPS). Themolecular basis for these diseases is mostly in the degradation pathwayfor HLGAGs. For instance, mucopolysaccharidosis type I involves a defectin iduronidase, which clips unsulfated iduronate residues from HLGAGchains. Similarly, persons suffering from mucopolysaccharidosis type II(MPS II) lack iduronate-2-sulfatase. In each of these disorders, markedchanges in the composition and sequence of cell surface HLGAGs occurs.Our methodology could be used as a diagnostic for these disorders toidentify which MPS syndrome a patient is suffering from.

Additionally the methods of the invention are useful for mapping proteinbinding HLGAG sequences. Analogous to fingerprinting DNA, the MALDI-MSsequencing approach may be used to specifically map HLGAG sequences thatbind to selected proteins. This is achieved by sequencing the HLGAGchain in the presence of a target protein as well as in the absence ofthe particular protein. In this manner, sequences protected fromdigestion are indicative of sequences that bind with high affinity tothe target protein.

The methods of the invention may be used to analyze branched orunbranched polymers. Analysis of branched polymers is more difficultthan analysis of unbranched polymers because branched carbohydrates, are“information dense” molecules. Branched polysaccharides include a fewbuilding blocks that can be combined in several different ways, thereby,coding for many sequences. For instance, a trisaccharide, in theory, cangive rise to over 6 million different sequences. The methods foranalyzing branched polysaccharides, in particular, are advanced by thecreation of an efficient nomenclature that is amenable to computationalmanipulation. Thus, an efficient nomenclature for branched sugars thatis amenable to computational manipulation has been developed accordingto the invention. Two types of numerical schemes that may encode thesequence information of these polysaccharides has been developed inorder to bridge the widely used graphic (pictorial) representation andthe proposed numerical scheme discussed below.

a. Byte-based (Binary-scheme) notation scheme. The first notation schemeis based on a binary numerical system. The binary representation inconjunction with a tree-traversing algorithm is used to represent allthe possible combinations of the branched polysaccharides. The nodes(branch points) are easily amenable to computational searching throughtree-traversing algorithms (FIG. 4A). FIG. 4A shows a notation schemefor branched sugars. Each monosaccharide unit can be represented as anode (N) in a tree. The building blocks can be defined as either (A),(B), or (C) where N1, N2, N3, and N4 are individual monosaccharides.Each of these combinations can be coded numerically to representbuilding blocks of information. By defining glycosylation patterns inthis way, there are several tree traversal and searching algorithms incomputer science that may be applied to solve this problem.

A simpler version of this notational scheme is shown in FIG. 4B. Thissimplified version may be extended to include all other possiblemodifications including unusual structures. For examples, an N-linkedglycosylation in vertebrates contains a core region (the tri-mannosylchitobiose moiety), and up to four branched chains from the core. Inaddition to the branched chains the notation scheme also includes othermodification (such as addition of fucose to the core, or fucosylation ofthe GlcNac in the branches or sialic acid on the branches). Thus, thesuperfamily of N-linked polysaccharides can be broadly represented bythree modular units: a) core region: regular, fucosylated and/orbisected with a GlcNac., b) number of branches: up to four branchedchains, each with GlcNac, Gal and Neu., and c) modifications of thebranch sugars. These modular units may be systematically combined togenerate all possible combinations of the polysaccharide. Representationof the branches and the sequences within the branches can be performedas a n-bit binary code (0 and 1) where n is the number ofmonosaccharides in the branch. FIG. 4C depicts a binary code containingthe entire information regarding the branch. Since there are up to fourbranches possible, each branch can be represented by a 3-bit binarycode, giving a total of 12 binary bits. The first bit represents thepresence (binary 1) or absence (binary 0) of the GlcNac residueadjoining the mannose. The second and the third bit similarly representthe presence or absence of the Gal and the Neu residues in the branch.Hence a complete chain containing GlcNac-Gal-Neu is represented asbinary (111) which is equivalent to decimal 7. Four of the branches canthen be represented by a 4 bit decimal code, the 1^(st) bit of thedecimal code for the first branch and the 2^(nd), the second branch etc(right).

This simple binary code does not contain the information regarding thelinkage (α vs. β and the 1-6 or 1-3 etc.) to the core. This type ofnotation scheme, however, may be easily expanded to include additionalbits for branch modification. For instance, the presence of a 2-6branched neuraminic acid to the GlcNac in the branch can be encoded by abinary bit.

b. Prime Decimal Notation Scheme: Similar to the binary notationdescribed above, a second computationally friendly numerical system,which involves the use of a prime number scheme, has been developed. Thealgebra of prime numbers is extensively used in areas of encoding,cryptography and computational data manipulations. The scheme is basedon the theorem that for small numbers, there exists a uniquely-definableset of prime divisors. In this way, composition information may berapidly and accurately analyzed.

This scheme is illustrated by the following example. The prime numbers2, 3, 5, 7, 11, 13, 17, 19, and 23 are assigned to nine common buildingblocks of polysaccharides. The composition of a polysaccharide chain maythen be represented as the product of the prime decimals that representeach of the building blocks. For illustration, GlcNac is assigned thenumber 3 and mannose the number 2. The core is represented in thisscheme as 2×2×2×3×3=72 (3 mannose and 2 GlcNacs). This notation,therefore, relies on the mathematical principle that 72 can be ONLYexpressed as the combination of three 2s and two 3s. The prime divisorsare therefore unique and can encode the composition information. Thisbecomes a problem when one gets to very large numbers but not an issuefor the size of numbers we encounter in this analysis. From this numberthe mass of the polysaccharide chain can be determined.

The power of the computational approaches of the notional scheme may beused to systematically develop an exhaustive list of all possiblecombinations of the polysaccharide sequences. For instance, anunconstrained combinatorial list of possible sequences of size m^(n),where m is the number of building blocks and n is the number ofpositions in the chain may be used. In FIG. 4C, there are 256 differentsaccharide combinations that are theoretically possible (4 combinationsfor each branch and 4 branches=4⁴).

A mass line of the 256 different polysaccharide structures may beplotted. Then the rules of biosynthetic pathways may be used to furtheranalyze the polysaccharide. In the example (shown in FIG. 4B), it isknown that the first step of the biosynthetic pathway is the addition ofGlcNac at the 1-3 linked chain (branch 1). Thus, branch 1 should bepresent for any of the other branches to exist. Based on this rule the256 possible combinations may be reduced using a factorial approach toconclude that the branch 2, 3, and 4 exist if and only if branch one isnon-zero. Similar constraints can be incorporated at the notation levelbefore generation of the master list of ensembles. With the notationscheme in place, experimental data can be generated (such as MALDI-MS orCE or chromatography) and those sequences that do not satisfy this datacan be eliminated. An iterative procedure therefore enables a rapidconvergence to a solution.

To identify branching patterns, a combination of MALDI-MS and CE (orother techniques) may be used, as shown in the Examples. Elimination ofthe pendant arms of the branched polysaccharide may be achieved by thejudicious use of exo and endoenzymes. All antennary groups may beremoved, retaining only the GlcNAc moieties extending from the mannosecore and forming an “extended” core. In this way, information aboutbranching is retained, but separation and identification of glycoformsis made simpler. One methodology that could be employed to form extendedcores for most polysaccharide structures is the following. Addition ofsialidases, and fucosidases will remove capping and branching groupsfrom the arms. Then application of endo-β-galactosidase will cleave thearms to the extended core. For more unusual structures, otherexoglycosidases are available, for instance xylases and glucosidases. Byaddition of a cocktail of degradation enzymes, any polysaccharide motifmay be reduced to its corresponding “extended” core. Identification of“extended” core structures will be made by mass spectral analysis. Thereare unique mass signatures associated with an extended core motifdepending on the number of pendant arms (FIG. 4D). FIG. 4D shows amassline of the “extended” core motifs generated upon exhaustive digestof glycan structures by the enzyme cocktail. Shown are the expectedmasses of mono-, di-, tri- and tetrantennary structures both with andwithout a fucose linked (α1→6 to the core GlcNAc moiety (from left toright); All of the “extended” core structures have a unique masssignature that is easily resolved by MALDI MS (from left to right).Quantification of the various glycan cores present may be completed bycapillary electrophoresis, which has proven to be a highly rapid andsensitive means for quantifying polysaccharide structures. [Kakehi, K.and S. Honda, Analysis of glycoproteins, glycopeptides andglycoprotein-derived polysaccharides by high-performance capillaryelectrophoresis. J Chromatogr A, 1996. 720(1-2): p. 377-93.]

EXAMPLES Example 1 Identification of the Number of Fragments Versus theFragment Mass for Di, Tetra, and Hexasaccharide

The masses of all the possible disaccharide, tetrasaccharide andhexasaccharide fragments were calculated and are shown in the mass lineshown in FIG. 5. The X axis shows the different possible masses of thedi, tetra and hexasaccharides and the Y axis shows the number offragments that having that particular mass. Although there is aconsiderable overlap between the tetra and hexasaccharide the minimumdifference in their masses is 13.03 D. Note that the Y axis has beenbroken to omit values between 17 and 40, to show all the bars clearly.

Example 2 Sequencing of an octasaccharide of HLGAG

Using hepI, hepII, hepIII, nitrous acid, and exoenzymes, such as2-sulfatase and (α-iduronidase, β-glucuronidase, n-deacetylase asexperimental constraints and the computer algorithm described above, anoctasaccharide (O2), two decasaccharide (FGF binding and ATIII binding)and a hexasaccharide sequence of HLGAG were sequenced.

1. Compositional Analysis of O2:

Compositional analysis of O2 was completed by exhaustive digest of a 30μM sample with heparinases I-III and analysis by capillaryelectrophoresis (CE). Briefly, to 10 μL of polysaccharide was added 200nM of heparinases I-III in sodium phosphate buffer pH 7.0. The reactionwas allowed to proceed at 30° C. overnight. For CE analysis the samplewas brought to 25 μL. Naphthalene trisulfonic acid (2 μM) was run as aninternal standard. Assignments of ΔU_(2S)—H_(NS,6S) and ΔU—H_(NS,6S)were made on the basis that they comigrated with known standards. Theinternal standard migrated between 4 and 6mins, the trisulfateddisaccharide ΔU_(2S)—H_(NS,6S) migrated between 6 and 8 mins and thedisulfated disaccharide ΔU—H_(NS,6S) migrated between 8 and 10 mins.Integration of the peaks indicated that the relative amounts of the twosaccharides was 3:1.

The CE data for O2 octasaccharide demonstrated that there is a majorpeak corresponding to the commonly occurring trisulfated disaccharide(ΔU_(2S)—H_(NS,6S)) and a small peak that corresponds to a disulfateddisaccharide (ΔU—H_(NS,6S)). The relative abundance of thesedisaccharide units obtained from the CE data shows that there are 3 Ds(±) and a 5 (±). The number of possible combination of sequences havingthese disaccharide units is 32. The possible combinations are shown inTable 4 below.

2. Digestion of O2 with Heparinase I:

Digestion of O2 was completed using both a short procedure and anexhaustive digest. “Short” digestion was defined as using 100 nM ofheparinase I and a digestion time of 10 minutes. “Exhaustive” digestionwas defined as overnight digestion with 200 nM enzyme. All digests werecompleted at room temperature. In the case of O2, both digest conditionsyield the same results. Short digestion with heparinase I yields apentasulfated tetrasaccharide (no acetyl groups) of m/z 5300.1 (1074.6)and a disaccharide of m/z4802.6 (577.1) corresponding to a trisulfateddisaccharide. This profile did not change upon exhaustive digest of O2.

Upon treatment with heparinase I, O2 is clipped to form fragments withm/z 4802.6 and 5,300.1. From the masses of these fragments it waspossible to uniquely determine that m/z of 4802.6 corresponded to atrisulfated disaccharide and m/z of 5300.1 corresponded to apentasulfated tetrasaccharide. Since the disaccharide composition of thesequence was known the only trisulfated disaccharide that may be formedis ±D and the possible pentasulfated tetrasaccharides that may be formedare ±5D, ±5-D, ±D5 and ±D-5. After identification of the fragments, thenext step was to arrange them to give the right sequence. Since this wasa cumbersome job to be handled manually a computer simulation was usedto progressively eliminate sequences from the master list that did notfit the experimental data. Using the rule that heparinase-I cleavesbefore and I_(2S) the heparinase-I digestion was simulated on thecomputer to generate the fragments for all the 32 sequences in themaster list. From the list of fragments formed for each sequence, thecomputer was used to search for fragments that corresponded to the diand-tetrasaccharide observed from the mass spectrometry data. Thesequences that gave the fragments that fit the mass spec data of hep Iare shown in FIG. 5 a. It may be observed from FIG. 5 a that all thesequences have 3 Ds which is consistent with the known rules for hepIdigestion used to produce these fragments. It may also be observed thattwo arrangements give the same product profile namely having the ±5(I—H_(NAc,6S) or G-H_(NS,6S)) the reducing end and having ±5 at thesecond position from the non-reducing end. To resolve this issue asecond experimental constraint, digestion with hepIII, was used.

Table 4 provides a list of sequences that satisfy the product profilesof hepI and hepIII digests of the octasaccharide O2. (a) shows thesequences that gave the di and tetrasaccharide fragments as observedfrom the mass spectrometry data. The fragments listed below along withtheir masses are those generated by computer simulation of hepI digest.(b) sequences in (a) that give the hexasaccharide fragment observed inthe mass spectrometry data after hepIII digestion. The fragments alongwith their masses were generated by computer simulation of hepIIIdigestion.

3. Digestion of O2 with Heparinase III:

Digestion of O2 with heparinase III yielded a nonasulfatedhexasaccharide of m/z 5958.7 (1731.9) and an unobserved disulfateddisaccharide (to conserve sulfates). Both short and exhaustive digestsyielded the same profile.

Heparinase III treatment of O2 resulted in a major fragment of m/z5958.7 which was uniquely identified as a hexasaccharide with 9 sulfategroups. The only sequence that satisfied the product profile of hepIIIdigestion was ±DDD-5 which is shown in Table 4. Table 4 shows that thereshould be a −5 (G-_(HNAc,6S)) in the reducing end. This was consistentwith the rule used for hepIII digestion, i.e. hepIII clips before a G.The masses shown in the table are integers. The masses used to searchfor the required fragments were accurate to two decimal places.

Thus it was possible to demonstrate the ability to converge to the finalsequence starting from the list of all possible sequences by eliminatingsequences that do not fit experimental data. Since the starting pointwas a list of all the possible sequences given the composition of asequence it was not possible that any sequences were missed during theanalysis.

Example 3 Sequencing of a Basic Fibroblast Growth Factor (FGF-2) BindingSaccharide

MALDI-MS of a basic fibroblast growth factor (FGF-2) binding saccharidewas performed to determine the mass and size of the saccharide as acomplex with FGF-2 (G. Venkataraman et al., PNAS. 96, 1892, (1999).).Dimers of FGF-2 bound to the saccharide (S) yielding a species with am/z of 37,009. By subtraction of FGF-2 molecular weight, the molecularmass of the saccharide was determined to be 2808, corresponding to adecasaccharide with 14 sulfates and an anhydromannitol at the reducingend.

1. Compositional Analysis:

Compositional analysis and CE of FGF-2 binding saccharide were completedas described above. Compositional analysis of this sample resulted intwo peaks corresponding to ±D (ΔU_(2S)H_(NS,6S)) and ±D′(ΔU_(2S)Man_(6S)) in the ratio 3:1. As this decasaccharide was derivedby nitrous acid degradation of heparin, the uronic acid at thenon-reducing end was not observed by CE (232 nm). Therefore, thenon-reducing end residue was identified as +D (I_(2S)H_(NS,6S)) bysequencing with exoenzymes. The number of possible sequences with thiscomposition is 16 Table 5(i). Of the 16 sequences, those that couldresult in the observed fragments upon heparinase I digestion of thedecasaccharide are shown in Table 5(ii). TABLE 5

2. Digestion with Heparinase I and Heparinase III:

To resolve the isomeric state of the internal uronic acid +D vs. −D,exhaustive digestion of the saccharide with heparinase I and heparinaseIII was performed. Heparinase I exhaustive digestion of the saccharideresults in only two species corresponding to a trisulfateddisaccharide(±D) and its anhydromannitol derivative, while heparinaseIII did not cleave the decasaccharide at all.

Heparinase I digestion of the decasaccharide yielded a pentasulfatedtetrasaccharide (m/z 5286.3) with an anhydromannitol at the reducing endand a trisulfated disaccharide of m/z 4804.6. Table 5 shows theconvergence of the FGF binding decasaccharide sequence. Thus, itprovides a list of sequences that satisfied the mass spectrometryproduct profiles of FGF-2 binding saccharide on treatment with hepI.Section (i) of Table 5 shows the master list of 16 sequences derivedfrom compositional analysis and exoenzyme sequencing of the non-reducingend. The disaccharide unit at the non-reducing end was assigned to be a+D using exoenzymes and the anhydromannitol group at the reducing end isshown as ‘. The mass of the fragments resulting from digestion ofdecasaccharide with heparinase I are shown in (ii). Also shown in (ii)are those sequences from (i) that satisfy heparinase I digestion data.Section (iii) of Table 5 shows the sequence of decasaccharide from (ii)that satisfies the data from exhaustive digestion using heparinase I.This product profile may be obtained only if there is a hepI cleavablesite at every position in the decasaccharide which led us to converge tothe final sequence DDDDD′ shown in section iii of Table 5. The abovetaken together confirm the sequence of the FGF-2 binding decasaccharidesequence to be DDDDD′ [(I_(2S)H_(NS,6S))₄I_(2S)Man_(6S)].

Example 4 Sequencing of an AT-III Binding Saccharide

An AT-III binding saccharide was used as an example of the determinationof a complex sequence.

1. Compositional Analysis:

Compositional analysis and CE were completed as described above.Compositional analysis of an AT-III binding saccharide indicated thepresence of three building blocks, corresponding to ΔU_(2S)H_(NS,6S)(±D), ΔUH_(NAc,6S) (±4) and ΔUH_(NS,3S,6S) (±7) in the relative ratio of3:1:1 respectively. The shortest polysaccharide that may be formed withthis composition corresponds to a decasaccharide, consistent with theMALDI-MS data. The total number of possible combinations of thistridecasulfated single acetylated decasaccharide sequences with theabove disaccharide building blocks is 320 Table 6. TABLE 6

2. Digestion with Heparinase I:

Digestion of this decasaccharide with heparinase I resulted in fourfragments. The major fragments include a decasulfated singly-acetylatedoctasaccharide (m/z 6419.7), a heptasulfated, singly acetylatedhexasaccharide with m/z 5842.1, a hexasulfated tetrasaccharide with m/zof 5383.1 and a trisulfated disaccharide (m/z 4805.3). Also present is acontaminant (*), a pentasulfated tetrasaccharide. The sequence of AT-IIIbinding decasaccharide has been reported to be D4-7DD, on the basis ofNMR spectroscopy (Y. Toida et al., J. Biol. Chem. 271, 32040 (1996)).Such a sequence should show the appearance of a tagged D or DD residueat the reducing end. However, we have found all the differentexperiments used in the elucidation of the decasaccharide sequence to beconsistent with each other in the appearance of a 4-7 tagged product andnot a D (or a DD) product. Surprisingly, this saccharide did not containan intact AT-III binding site, as proposed. Therefore, confirmation ofthe proposed sequence was sought through the use of integral glycansequencing (IGS) methodology. The result of IGS agreed with ouranalysis. A minor contaminant saccharide has also been found. Of the 320possible sequences, only 52 sequences satisfied heparinase I digestiondata Table 6(i). The mass spectrum of the exhaustive digestion of thedecasaccharide with heparinase I showed m/z values that corresponded toa trisulfated disaccharide and a octasulfated hexasaccharide, therebyfurther reducing the list of 52 sequences to 28 sequences Table 6(ii).

3. Digestion with Heparinase II:

To further converge on the sequence, a ‘mass-tag’ was used at thereducing end of the saccharide (Δ m/z of 56.1 shown as ‘t’). Thisenabled the identification of the saccharide sequence close to and atthe reducing end. Typical yields for the mass-tag labeling variedbetween 80-90% as determined by CE. Treatment of the semicarbazidetagged decasaccharide, with heparinase II resulted in the followingproducts: m/z 5958.4 (nine sulfated hexasaccharide), m/z 5897.7 (taggedheptasulfated, singly acetylated hexasaccharide), m/z 5380.1(hexasulfated tetrasaccharide), m/z 5320.9 (tagged tetrasaulfatedtetrasaccharide), m/z 5264.6 (tetrasulfated tetrasaccharide) and m/z4805.0 (a trisulfated disaccharide). The m/z value of 5320.9 and 5897.7corresponded to a tagged tetrasulfated tetrasaccharide and a taggedheptasulfated hexasaccharide, both containing the N-acetyl glucosamineresidue. This result indicated that ±4 (I/GH_(NAc,6S)) is present at thereducing or one unit from the reducing end, thereby limiting the numberof possible sequences from 28 to 6 Table 6(iii).

4. Digestion with Nitrous Acid:

Partial nitrous acid digestion of the tagged as well as the untaggeddecasaccharide provided no additional constraints but confirmed theheparinase II data. Exhaustive nitrous acid digestion, however, gaveonly the reducing end tetrasaccharide (with and without the tag) as anunclipped product. Exhaustive nitrous acid treatment of decasaccharideessentially gives one tetrasulfated single-acetylated anhydromannitoltetrasaccharide species (one tagged m/z 5241.5 and one untagged m/z5186.5). This confirmed that ±4 (I/GH_(NAc,6S)) is one unit away fromthe reducing end. Sequential use of exoenzymes uniquely resolved theisomeric state of the uronic acid as +4 and the reducing enddisaccharide to be −7 consistent with 4-7 being the key AT-III bindingmotif. Treatment of this tetrasaccharide with iduronidase (and notglucuronidase) resulted in a species of m/z 5007.8 corresponding to theremoval of iduronate residue. Further treatment with exoenzymes only inthe following order (glucosamine 6-O sulfatase, hexosamidase andglucuronidase) resulted in the complete digestion of the trisaccharide.Table 6 shows the convergence of the AT-III binding decasaccharidesequence from 320 possible sequences to 52 to 28 to 6 to the finalsequence. Thus, the sequence of the AT-IlI binding decasaccharide wasdeduced as ±DDD4-7(ΔU_(2S)H_(NS,6S)I_(2S)H_(NS,6S)I_(2S)H_(NS,6S)IH_(NAc,6S)GH_(NS,3S,6S)).

Example 5 Sequencing of a Hexasaccharide1 of HLGAG

10 pM H1 was treated with 2 mM nitrous acid in 20 mM HCl at roomtemperature for 20 minutes such that limited degradation occurred. After20 minutes, a two-fold molar excess of (arg-gly)₁₉arg in saturatedmatrix solution was added. 1 pmol of saccharide was spotted and used formass spectrometric study. All saccharides were detected as non-covalentcomplexes with (arg-gly)₁₉arg. Starting hexasaccharide was observed aswas a tetrasaccharide and disaccharide. Also observed is uncomplexedpeptide (not shown in figures). Hereafter two m/z values are reported.The first is the observed m/z value that corresponds to thesaccharide+peptide. The second number in parentheses is the m/z of thesaccharide alone obtained by subtracting the mass of the peptide.

After 20 minutes, nitrous acid treatment of H1 yielded starting materialat m/z 5882.5 (1655.8) which corresponded to a hexasaccharide with 8sulfates and an anhydromannitol at the reducing end, a m/z 5304.1(1077.3), which corresponded to a tetrasaccharide with theanhydromannitol at the reducing end and a m/z of 4726.2 (499.4) whichcorresponded to a disulfated disaccharide with the anhydromanitol at thereducing end.

This sample was then subjected to exoenzyme analysis. Three exoenzymeswere added—iduronate 2-O sulfatase, iduronidase, and glucosamine 6-Osulfatase. The nitrous acid sample was neutralized via addition of ⅕volume of 200 mM sodium acetate 1 mg/mL BSA pH 6.0 after which theenzymes were added. Glucosamine 6-O sulfatase was added after digestionwith the first two enzymes was complete. Final enzyme concentrationswere in the range of 20-40 milliunits/mL and digestion was carried outat 37° C. for a minimum of two hours.

Upon incubation with iduronate 2-O sulfatase and iduronidase, thehexasaccharide and tetrasaccharide peaks were reduced in mass. Thedisaccharide was no longer detectable after incubation with the enzymes.The hexasaccharide gave a new species at m/z 5627.3 (1398.8)corresponding to loss of sulfate and iduronate. The tetrasaccharideyielded a species of m/z 5049.3 (820.8) again corresponding to loss ofsulfate at the 2-O position and loss of iduronate. These data showedthat all the disaccharide building blocks contained an I2S.

Addition of glucosamine 6-O sulfatase and incubation overnight at 37° C.resulted in the production of two new species. One at m/z 5546.8(1318.3) resulting from loss of sulfate at the 6 position on glucosamineand the other at n/z 5224.7 (996.2), again corresponding to atetrasaccharide 6-O sulfate. These data showed that except for thereducing end anhydromanitol containing disaccharide unit the other unitscontained HNS. The data indicated that the sequence is DDD′, indicatingthat this sequence was originally derived from nitrous acid degradationunlike the other sequences which were derived from degradation by theheparinases.

Example 6 Sequencing of Other Complex Polysaccharides

The sequencing approach may be readily extended to other complexpolysaccharides by developing appropriate experimental constraints. Forexample, the dermatan/chondroitin mucopolysaccharides (DCMP) consistingof a disaccharide repeat unit is amenable to a hexadecimal coding systemand MALDI-MS. Similar to what is observed for HLGAGs, there is uniquesignature associated with length and composition to a given mass inDCMP. For instance, the minimum difference between any disaccharide andany tetrasaccharide is 139.2 Da, therefore, the length, the number ofsulfates and acetates may be readily assigned for a given DCMpolysaccharide up to an octa-decasaccharide. Similarly, in the case ofpolysialic acids (PSA), present mostly as homopolymers of5-N-acetylneuraminic acid (NAN) or 5-N-glycolylneuraminic acid (NGN),the hexadecimal coding system may be easily extended to NAN/NGN toencode the variations in the functional groups and enabling a sequencingapproach for PSA.

1. Dermatan/Chondroitin Family of Complex Mucopolysaccharides

DCMP are found in dense connective tissues such as bone and cartilage.The basic repeat unit of the dermatan/chondroitin mucopolysaccharides(DCMP) may be represented as -(β1→4) U_(2X)-(α/β1→3) Gal_(NAc,4X,6X)-,where U is uronic acid, Gal_(NAc) is a N-acetylated galactosamine. Theuronic acid may be glucuronic acid (G) or iduronic acid (I) and sulfatedat the 2-O position and the galactosamine (GalNAc) may be sulfated inthe 4-O or the 6-O position, thereby resulting in 16 possiblecombinations or building blocks for DCMP. Like the heparinases thatdegrade HLGAGs, there are distinct chondoroitinases and other chemicalmethods available that clip at specific glycosidic linkages of DCMP andserve as experimental constraints. Furthermore, since DCMPs are acidicpolysaccharides, the MALDI-MS techniques and methods used for HLGAGs maybe readily extended to the DCMPs.

PEN scheme and mass-identity relationships for DCMP: Shown in Table 7are the property-encoded nomenclature (PEN) of the 16 possible buildingblocks of dermatan/chondroitin family of molecules. The sequencingapproach enables one to establish important mass-identity relationshipsas well as master list of all possible DCMP sequences from disaccharidesto dodecasaccharides. These are plotted as a mass line as shown in FIG.5. As observed for HLGAGs, there is a unique signature associated withlength and composition for a given mass. As described above the minimumdifference between any disaccharide and any tetrasaccharide was found tobe 101 Daltons for HLGAGs. Interestingly, in the case of DCMP theminimum difference between any disaccharide and any tetrasaccharide is139.2 Da. Therefore, the length, the number of sulfates and acetates maybe readily assigned for a given DCM polysaccharide up to anocta-decasaccharide. TABLE 7 ALPH I/G 2X 6X 4X CODE DISACC MASS (ΔU) 0 00 0 0 I-Gal_(NAc) 379.33 0 0 0 1 1 I-Gal_(NAc, 4S) 459.39 0 0 1 0 2I-Gal_(NAc, 6S) 459.39 0 0 1 1 3 I-Gal_(NAc, 4S, 6S) 539.45 0 1 0 0 4I_(2S)-Gal_(NAc) 459.39 0 1 0 1 5 I_(2S)-Gal_(NAc, 4S) 539.45 0 1 1 0 6I_(2S)-Gal_(NAc, 6S) 539.45 0 1 1 1 7 I_(2S)-Gal_(NAc, 4S, 6S) 619.51 10 0 0 −0 G-Gal_(NAc) 379.33 1 0 0 1 −1 G-Gal_(NAc, 4S) 459.39 1 0 1 0 −2G-Gal_(NAc, 6S) 459.39 1 0 1 1 −3 G-Gal_(NAc, 4S, 6S) 539.45 1 1 0 0 −4G_(2S)-Gal_(NAc) 459.39 1 1 0 1 −5 G_(2S)-Gal_(NAc, 4S) 539.45 1 1 1 0−6 G_(2S)-Gal_(NAc, 6S) 539.45 1 1 1 1 −7 G_(2S)-Gal_(NAc, 4S, 6S)619.51

Table 7 shows the Property Encoding Numerical scheme used to code DCMPs.The first column codes for the isomeric state of the uronic acid (0corresponding to iduronic and 1 corresponding to glucuronic). The secondcolumn codes for the substitution at the 2-O position of the uronic acid(0-unsulfated, 1-sulfated). Columns 3 and 4 code for the substitution atthe 4 and 6 position of the galactosamine. Column 5 shows the numericcode for the disaccharide unit, column 6 shows the disaccharide unit andcolumn 7 shows the theoretical mass calculated for the disaccharideunit.

Tools as experimental constraints: Similar to the heparinases thatdegrade HLGAGs there are chondroitinases that degrade chondroitin-likeand dermatan-like regions of DCMP. The chondroitinases B, C, AC and ABChave distinct specificities with some overlap. For the most partchondroitinases cover the entire range of linkages found in DCMP. Thereare several chondroitinases that have been isolated and cloned fromdifferent sources. In addition to the enzymes, there are a fewwell-established chemical methods that may be used to investigate DCMP.These include nitrous acid treatment. Thus there are adequate tools(enzymatic and chemical) which function as ‘experimental constraints’ toenable DCMP sequencing. Below we use two DCMP sequences to illustratesequencing DCMP.

A. Serpin HCF-2 binding DCMP Hexasaccharide):

The minimum size DCMP binding to serpin HCF-2 was isolated and itscomposition was determined using elaborate methods which included anionexchange chromatography, paper electrophoresis and paper chromatography.The sequencing strategy through the integration of PEN and MSestablished the identity of this serpin HCF-2 binding saccharide to be ahexasaccharide with 6 sulfates and 3 acetates. The high degree ofsulfation pointed to a dermatan-like saccharide. Since this saccharidewas derived using partial N-deacetylation and nitrous acid treatment, itcomprises a 5 membered anhydrotalitol ring at the reducing end.Composition analysis of the saccharide may be obtained by degradationusing the chondroitinases. The composition shows the presence ofΔU_(2S)Gal_(NAc,4S) (±5) and ΔU_(2S)aTal_(4S) (aTal-anhydrotalitol-±5′)in a 2:1 ratio. This enabled the generation of a master list with 8possible sequences as shown in Table 8a. 2-sulfatase and iduronidasetreatment of the hexasaccharide produced a shift in the mass spectrumcorresponding to the loss of a sulfate and iduronate, thereby fixing theI_(2S) at non-reducing end (Table 8b). In order to converge further,Chondroitinase B (which acts on iduronate residues in dermatan-likeregions) was used and a single peak in the mass spectrum correspondingto a 2-sulfated disaccharide was observed. This led us to converge tothe sequence +555′(I_(2S)-Gal_(NAc,4S)I_(2S)-Gal_(NAc,4S)-I_(2S)-aTal_(4S)). TABLE 8

B. Hypothetical:

In this example a “hypothetical DCMP polysaccharide” which is morecomplex than the previous example is used. Assume that MS yields aresult that is interpreted to be an octasaccharide with 8 sulfates and 4acetates, and that the composition analysis points to three speciescorresponding to ΔU_(2S)Gal_(NAc,4S) (±5), ΔUGal_(NAc,6S) (±2) andΔU_(2S)Gal_(NAc,4S,6S) (±7) in 2:1:1 relative abundance. This enablesone to generate a master-list, which would point to 96 possiblesequences (Table 9a). It is expected that the digestion of thesaccharide sample with chondroitinase AC would result in two productswith masses that would correspond to two tetrasulfated tetrasaccharideunits and thereby reduce the master list to 4 possible sequences (Table9b). Complete deamination using hydrazonolysis and nitrous acidtreatment would result in 3 peaks, two corresponding to a disulfateddisaccharide and the third corresponding to a trisulfated disaccharide.Treatment of the degraded products with 2-sulfatase and iduronidase (andnot glucuronidase) should result in peaks that correspond to the loss ofsulfate and iduronate residues. This would enable the identification ofthe isomeric state of 5 and 7 thereby converging the master list to onesequence ±55-27(ΔU_(2S)-Gal_(NAc,4S)-I_(2S)-Gal_(NAC,4S)-G-Gal_(NAC,6S)-I_(2S)-Gal_(NAc,4S,6S)).TABLE 9

It is important to reiterate that, similar to what was developed forHLGAG, distinct or additional ‘convergence strategies or experimentalconstraints’ may be used to arrive at the ‘unique’ solution for DCMP.

2. Polysialic Acid

Polysialic acids are linear complex polysaccharides found as a highlyregulated post-translational modification of the neural cell adhesionmolecule in mammals that are present mostly as homopolymers of5-N-acetylneuraminic acid (NAN) or 5-N-glycolylneuraminic acid (NGN).The monomeric units of NAN and NGN are linked by α 2-8 glycosidiclinkages, and may be modified at the 4-O, 7-O, and 9-O positions. Themajor modification is acetylation. In addition, much rarer modificationsincluding sulfation and lactonization occur at the 9-O position. Adeaminated form of neuraminic acid namely 5-deamino-3,5-dideoxyneurmanicacid (KDN) has also been discovered. The PEN-MS sequencing approach isextended to polysialic acids, and using NAN and NGN units we illustratehow this is achieved.

PEN scheme and mass-identity relationships for PSA: PSA is comprised oftwo different monomeric repeats, with variations in the modification ofeach unit. The flexibility of the PEN enables easy adaptation to amonomeric repeat unit for PSA from the dimeric repeats for HLGAG andDCMP. The PEN scheme for PSA is shown in Table 10. The sequencingapproach establishes important mass-identity relationships as well asmaster list of all of the combinations of monomeric units for NAN andNGN. The mass-line for polymeric units of NAN and NGN are shown in FIGS.6A and B. Note that there is a considerable overlap in masses observedfor the higher order oligomers of both NAN and NGN (FIGS. 6A and B). Theminimum difference in the masses between a n 'mer and a n+1'merstabilizes at 3.01 Da for NAN and 13 Da for NGN, as we go to tetra,penta and hexasaccharide, thereby providing a safe margin for detectionof these fragments using MS. TABLE 10 NAN/ NGN 9X 7X 4X Code Saccharideunit Mass 0 0 0 0 0 NAN 309.28 0 0 0 1 1 NAN_(4Ac) 351.32 0 0 1 0 2NAN_(7Ac) 351.32 0 0 1 1 3 NAN_(4Ac,7Ac) 393.36 0 1 0 0 4 NAN_(9Ac)351.32 0 1 0 1 5 NAN_(4Ac,9Ac) 393.36 0 1 1 0 6 NAN_(7Ac,9Ac) 393.36 0 11 1 7 NAN_(4Ac,7Ac,9Ac) 435.40 1 0 0 0 −0 NGN 325.27 1 0 0 1 −1NGN_(4Ac) 367.32 1 0 1 0 −2 NGN_(7Ac) 367.32 1 0 1 1 −3 NGN_(4Ac,7Ac)409.36 1 1 0 0 −4 NGN_(9Ac) 367.32 1 1 0 1 −5 NGN_(4Ac,9Ac) 409.36 1 1 10 −6 NGN_(7Ac,9Ac) 409.36 1 1 1 1 −7 NGN_(4Ac,7Ac,9Ac) 451.40

Shown in Table 10 is the Property Encoded Numerical scheme for PSA.Column 1 codes for whether the monomeric unit is NAN or NGN. Columns 2,3and 4 code for the variations in the 9, 7 and 4 positions respectively,where 1 corresponds to acetylated and 0 corresponds to unacetylated.Column 5 shows the numeric code for the PSAs. −0 to −7 was used insteadof 8-F. Assigning the numbers to code for the variability in acetylationand the sign would indicate if it is NAN/NGN. Column 6 lists themonosaccharide represented by the code in column 5. Column 7 lists thetheoretical mass calculated for the monomeric units shown in column 6.

The mass-line for the combinations of substituted/unsubstituted NANcontaining monomeric units in PSA is shown in FIG. 6A. The X-axisrepresents the calculated masses for monosaccharide to hexasaccharides.Shown in the Y axis is the number of fragments of a particular lengthand composition that exists for a given mass. The values 150-190 wereomitted to improve the clarity of the other peaks. The minimumdifference between any monosaccharide and any disaccharide is 165.2 Da,between any di and any trisaccharide is 39.03 Da, between any tri andany tetrasaccharide is 39.03 Da and 3.01 Da for all higher ordersaccharides.

The mass-line for the combinations of substituted/unsubstituted NGNmonomeric units in PSA is shown in FIG. 6B. The X-axis represents thecalculated masses for monosaccharaide to hexasaccharide. Shown in the Yaxis is the number of fragments of a particular length and compositionthat exist for a given mass. The values 150-190 were omitted to improvethe clarity of the other peaks. The minimum difference between anymonosaccharide and any disaccharide is 181.2 Da, between any di and anytrisaccharide is 55.03 Da and 13 Da for higher order saccharides.

Tools as experimental constraints: There are several tools and detectionmethods available for studying PSAs. Based on the properties of thebuilding blocks of PSA, this class of linear polysaccharides is amenablefor MS. Methods of purifying PSA polymers and obtaining compositionusing HPLC, CE and mass spectrometry have very recently beenestablished. Enzymatic tools from various sources have been used tostudy PSA extensively. Notably the bacterial exosalidase which cleavePSA polymers processively from the non-reducing end and thebacteriophage derived endoneuramidase, which clips endolytically boththe NAN and NGN containing PSA linear polysaccharides. In addition tothese enzymes chemical methods such as hydrozonolysis followed bynitrous acid treatment and periodate oxidation followed by sodiumborohydrate treatment may be used to as tools to degrade PSApolysaccharides into smaller polysaccharides.

Example 7 Variation of Experimental Conditions Resulting in Alterationof Enzymatic Reactions and its Effect on the Methods of the Invention

Secondary specificities of the heparinases have been observed,especially under exhaustive degradation conditions. As a part of ongoinginvestigations into the enzymology of heparinases, the relative rates ofcleavage of I and G containing sites by heparinase I and III withdefined substrates under different conditions have been measured. Forinstance heparinase III cleaves both at I and G containing linkages andnot I_(2S) [H. E. Conrad, Heparin Binding Proteins (Academic Press, SanDiego, 1998).]. However, under the reaction conditions used in thisstudy, there is a dramatic (8-10 fold) difference in the rates ofcleavage, with I-containing linkages being clipped more slowly thanG-containing linkages (FIG. 7A). FIG. 7A shows cleavage by recombinantheparinase III of tetrasaccharides containing either G (●), I(∘) orI_(2S) (♦) linkages. Each reaction was followed by capillaryelectrophoresis. With these substrates, heparinase III does not cleaveI_(2S)-containing glycosidic linkages, and cleaves G-containing linkagesroughly 10 times as fast as I-containing linkages. Under the “short”conditions of digest it is expected that only G-containing saccharidesare cleaved to an appreciable extent. [Conditions for enzymatic digestof HLGAG oligosaccharides were set forth above, briefly, Digests wereeither designated as “short” or “exhaustive”. Short digests werecompleted with 50 nM enzyme for 10 minutes. Exhaustive digests werecompleted using 200 nM enzyme for either four hours or overnight.Partial nitrous acid cleavage was completed using a modification ofpublished procedures. Briefly, to an aqueous solution of saccharide wasadded a 2× solution of sodium nitrite in HCl such that the concentrationof nitrous acid was 2 mM and HCl was 20 mM. The reaction was allowed toproceed at room temperature with quenching of aliquots at various timepoints via the addition of 1 μL of 200 mM sodium acetate 1 mg/mL BSA pH6.0. Exhaustive nitrous acid was completed by reacting saccharide with 4mM nitrous acid in HCl overnight at room temperature. In both cases, itwas found that the products of nitrous acid cleavage could be sampleddirectly by MALDI without further cleanup and without the need to reducethe anhydromannose residues to anhydromannitol. The entire panel ofHLGAG degrading exoenzymes were purchased from Oxford Glycosystems(Wakefield, Mass.) and used as suggested by the manufacturer.] Forexample, with the hexasaccharide ΔUH_(NH,6S)GH_(NS)IH_(NAc), (whichcontains both I and G in a minimally sulfated region) cleavage occursonly at the G under “short” digest conditions as shown in Table II.TABLE II Species m/z (+Peptide) Observed ΔUH_(NH,6S)GH_(NS)IH_(Nas)5442.1 √ ΔUH_(NS)IH_(NAs) 5023.6 √ ΔUH_(NH,6S)GH_(NS) 5061.7

Heparinase II was incubated with the hexasaccharideΔUH_(NH,6S)GH_(NS)IH_(Nac) and only cleavage at the G and not the I wasobserved. Furthermore, we have found that degree of sulfation doesaffect the kinetics of heparinase III degradation of oligosaccharides[S. Ernst et al., Crit. Rev. Biochem. Mol. Biol. 30, 387 (1995); S.Yamada et al., Glycobiology 4, 69 (1994); U. R. Desai, H. M. Wang, R. J.Linhardt, Biochemistry 32, 8140 (1993); R. J. Linhardt et al.,Biochemistry 29, 2611 (1990).]. In the case of heparinase I, this enzymedoes not clip either I or G-containing glycosidic linkages within thecontext of our experimental procedures, whereas it readily clips I_(2S)containing polysaccharides (FIG. 7B). FIG. 7C shows the same study ascompleted in (A) except heparinase I was used instead of heparinase III.With heparinase I, cleavage only occurs at I_(2S)-containing linkagesbut not before I or G. There is only one report of heparinase I clippingG_(2S) containing linkages [S. Yamada, T. Murakami, H. Tsuda, K.Yoshida, K. Sugahara, J. Biol. Chem. 270, 8696 (1995).], which wastested with two tetrasaccharide substrates and the experiments wereperformed under conditions which are kinetically very different from the‘short’ heparinase I digestion, presented here.

Quite a few factors have severely limited and complicated prior artstudies and interpretation of heparinase substrate specificityexperiments. First, not only is a homogenous substrate preparationdifficult, but also analyzing the substrates and products have been verychallenging. Analysis has primarily relied on co-migration of thesaccharides with known standards, and as others and we have observed,oligosaccharides with different sulfation patterns do co-migrate,complicating unique assignments. Further, some oligosaccharides used inprevious studies to assign substrate specificity for the heparinaseswere not homogeneous, complicating analysis. The development of theMALDI-MS procedure of the invention has enabled rapid and accuratedetermination of the saccharides. The second problem is the preparationof pure wild-type heparinases from the native host. The wild-typeheparinase is isolated from Flavobacterium heparinum and this organismproduces several complex polysaccharide-degrading enzymes, and oftenthese copurify with each other. For example, when examining the,kinetics of heparinase III, we found that a commercial source ofheparinase III was able to degrade the supposedly non-cleavableΔU_(2S)H_(NS,6S)I_(2S)H_(NS,6S). Furthermore, MS and CE analysis of theproducts indicated that one was specifically 2-O desulfated suggesting asulfatase contamination. Recombinant heparinase III produced andpurified in our laboratory (and not having contamination with otherheparin degrading enzymes) does not cleaveΔU_(2S)H_(NS,6S)I_(2S)H_(NS,6S) as expected. Thus, different enzymepreparations and differences in digestion conditions, and differences insubstrate size and composition and often contaminating substrates, takentogether with assignments based on co-elution make comparison of datanot only very difficult but also has led to contradictory findings.

Regardless of the outcome of heparinase substrate specificities, thereare other methods that may be used to extract the isomeric state of theuronic acid [I or G or I_(2S) or G_(2S)]. The uronic acid component ofeach disaccharide unit may be unambiguously ascertained by completingcompositional analysis after exhaustive nitrous acid treatment. By thismethod, compositional analysis of given oligosaccharides may beaccomplished and the presence of G_(2S), I_(2S), I and G containingbuilding blocks assessed. With this information, rapid convergence to asingle sequence could be completed by judicious application of theheparinases (regardless of their exact substrate specificity), sincecleavage would give mass information on either side of the cleavagesite. Thus, in the octasaccharide (example 1) case, application ofexhaustive nitrous acid would yield 1×ΔUMan_(6S), 2×I_(2S)Man_(6S) and1×GMan_(6S). Then, digestion of this octasaccharide, after tagging, withheparinase III under any conditions (forcing or non-forcing) wouldresult in the formation of a hexasaccharide m/z 5958.7 and adisaccharide, immediately fixing the sequence. A similar sequence ofevents may be used with heparinase I to converge to a single sequencefor the octasaccharide.

While there are caveats to the use of any one particular system forsequence analysis, whether the system is chemical degradation orenzymatic analysis, the sequencing strategy presented here is notcritically dependent on any, single technique. One of the majorstrengths of the sequencing strategy of the invention is the flexibilityof our approach and the integration of MALDI and the coding scheme whichenable the ability to adapt to different experimental constraints [Forexample, the recently cloned mammalian heparanase is another possibleexperimental constraint. M. D. Hulett et al., Nat. Med. 5,793 (1999); I.Vlodavsky et. al., Nat. Med. 5, 803 (1999).]. As stated additional ordifferent sets of experimental constraints may be used to not onlyarrive at a unique solution but also may be used to validate or confirmthe solution from a given set of experimental constraints.

Example 8 Methods for Identifying Protein-Polysaccharide Interactionsand Improved Methods for Sequencing

To identify HLGAG sequences that bind to a particular protein, the mostcommon methodology involves affinity fractionation of oligosaccharidesusing a particular HLGAG subset, namely porcine intestinal mucosaheparin. Enzymatically or chemically derived heparin oligosaccharides ofa particular length are passed over a column of immobilized protein.After washing, the bound fraction is eluted using high salt to disruptinteractions between the sulfates on the polysaccharide and basicresidues on the protein; interactions which are crucial for binding.Eluted oligosaccharides are then characterized, typically by NMR. Inthis manner, sequences that bind to a number of proteins, includingantithrombin III (AT-III), basic fibroblast growth factor (FGF-2), andendostatin have been identified.

While rigorous and well tested, this approach suffers from a number oflimitations. First, column chromatography requires large (milligram)amounts of material for successful analysis. Of the entire family ofHLGAGs, only heparin is available in these quantities. However, heparin,due to its high sulfate content, contains a limited number of sequences,biasing the selection procedure. Thus, there is no opportunity to sampleor select for unusual sequences that might in fact bind with highaffinity. In vivo HLGAG-binding proteins sample and bind to the morestructurally diverse heparan sulfate (HS) chains of proteoglycans at thecell surface where heparin-like sequences (i.e., sequences with a highdegree of sulfation) do not always predominate. Heparin, whilestructurally related to HS, is present in vivo only in mast cells. Forthese reasons, heparin is not always an appropriate analog of cellsurface HS, and in fact, the exclusive use of heparin in affinityfractionation experiments has created confusion in the field. Oneexample illustrates this point. FGF-2 binds to a specific subset ofheparan sulfate sequences that contain a critical 2-O sulfated iduronateresidue. Column chromatography-has separated a high affinity binder ofFGF-2, the sequence(s) of which have been identified as oligosaccharidescontaining the predominant trisulfated disaccharide[I_(2S)H_(NS,6S)]_(n) (n=3-6). However, rigorous examination of thecrystal structures of FGF-2, including co-crystals of FGF with HLGAGoligosaccharides, indicates that only three contacts between sulfatesand basic residues on FGF-2 are important for high affinity binding.

Using the mass spectrometric approach of the invention we have developedan improved way to identify polysaccharide-protein interactions. Theadvantage of this approach is that it is highly sensitive, requiringonly picomoles of material, which may be isolated from in vivo sources.As described below the approach may be used for the identification andsequencing of oligosaccharides that bind to proteins using picomoles ofmaterial. As a proof of concept, we show herein that this novelmethodology is functionally equivalent to the established columnaffinity fractionation method for three proteins: FGF-1, FGF-2 andATIII, using heparin oligosaccharides as a model system. Furthermore, weshow herein that this system can be extended such that heparan sulfateisolated from the cell surface can be used to isolate binding proteins,demonstrating that, for the first time, unbiased, biologically relevantHLGAGs can be used to identify binding sequences.

Methods:

Protein preparation and immobilization. ATIII was incubated overnightwith excess porcine mucosal heparin, then biotinylated with EZ-linksulfo-NHS biotin (Pierce). Canon NP Type E transparency film was tapedto the MALDI sample plate and used as a protein immobilization surface.FGF-1 and FGF-2 were immobilized by spotting 1 μl of aqueous solution onthe film and air-drying. ATIII was immobilized by first drying 4 μgneutravidin on the film surface, then adding biotinylated ATIII to theneutravidin spot. Heparin was removed by washing ten times with 1M NaCland ten times with water.

Saccharide binding, selection and analysis. Saccharides were derivedfrom a partial digest of porcine mucosal heparin by heparinase I. Thehexasaccharide fraction was obtained by size exclusion chromatography onBiogel P-6 and lyophilized to dryness. Saccharides were bound toimmobilized proteins by spotting 1 μl of aqueous solution on the proteinspot for at least five minutes. Unbound saccharides were removed bywashing with water fifteen times. For selection experiments, the spotwas washed ten times with various NaCl concentrations, followed by tenwater washes. Caffeic acid matrix in 50% acetonitrile with 2 pmol/μl(RG)₁₉R was added to the spot prior to MALDI analysis. All saccharideswere detected as noncovalent complexes with (RG)₁₉R using MALDIparameters described herein.

Saccharide digestion by heparinase I or III. Saccharides selected forFGF-2 binding were digested with heparinases I or III by spotting 8μg ofenzyme in water after selection was completed. The spot was kept wet forthe desired digestion time by adding water as necessary. Caffeic acidmatrix with 2 pmol/μl (RG)₁₉R was added to the spot for MALDI analysis.

Isolation, Purification, and Selection of FGF binders from SMC heparansulfate. Bovine aortic smooth muscle cells (SMCS) were grown toconfluency. Cells were washed twice with PBS and then 200 nM heparinaseIII was added for 1 hr. The supernatant was heated to 50° C. for 10minutes to inactivate heparinase III and filtered. To removepolynucleotide contamination, the samples were treated with DNAse andRNAse at room temperature overnight. Heparan sulfate was isolated bybinding to a DEAE filter, washing away unbound material, and elutionusing 10 mM sodium phosphate 1M NaCl pH 6.0. The material was thenconcentrated and buffer exchanged into water using a 3,000 MWCOmembrane. The retentate was lyophilized and reconstituted in water. 100nM heparinase II was added and aliquots were taken at 5, 10, 20, and 30minutes post-addition. 1 μL was spotted on FGF. After drying, the samplewas washed, 2 pmol/μl (RG)₁₉R in matrix was added, and the sample wasanalyzed as outlined above.

Results:

Saccharide binding to FGF-2 and FGF-1. As a first step towards thedevelopment of a viable MALDI selection procedure, the FGF system usingits prototypic members, viz. FGF-1 and FGF-2 was selected. Initialexperiments involved the use of a purified polysaccharide (Hexa 1 ofTable 12) that is known to bind with high affinity to FGF. With FGF-2,we found that Hexa 1 binds to FGF-2 and were detected, even with a saltwash of 0.5M NaCl, consistent with the known affinity of Hexa 1 forFGF-2. In addition, when an equimolar mixture of Hexa 1 and Hexa 2 (alow affinity binder) were applied to FGF-2 and washed with 0.2M NaCl toeliminate nonspecific binding, only Hexa 1 was observed. Together, theseresults point to the fact that, under of the conditions of theexperiment, immobilized FGF-2 retained the same binding specificity asFGF in solution. Further demonstrating that binding specificity wasintact, heat denaturation of FGF resulted in the detection of nosaccharide binders. TABLE 12 Saccharide Sequence Hexa 1 (a) ±DDD or (b)DDMan_(6S) Hexa 2 ±D4-7 Penta 1

FGF affinity fractionation of a hexasaccharide mixture derived from theenzymatic depolymerization of heparin was used to enrich for FGFbinders. To determine whether specific binders could be selected from amore complex mixture using our methodology, a hexasaccharide fractionderived from incomplete heparinase I digestion of porcine intestinalmucosa heparin was spotted on immobilized FGF. At least five uniquestructures were detected in the unfractionated hexasaccharide mixture.Upon a salt wash, only two structures, 8- and 9-sulfatedhexasaccharides, remained. Importantly, the same results couldalternately be achieved by enriching the spot for specific binders andcompeting off low affinity binders. FGF-1, which has been shown to havesimilar binding properties as FGF-2, could also select for the octa- andnonasulfated hexasaccharides from a mixture.

Sequencing saccharides on the MALDI surface. The highly sensitivesequencing methodology of the invention was used to test whether wecould derive structural information of FGF high affinity binders ontarget. The octa- and nonasulfated saccharides were subjected toenzymatic and chemical depolymerization. After saccharide selection, thesaccharide sample was depolymerized by heparinase I to obtain sequenceinformation. The nonasulfated hexasaccharide was reduced to a singletrisulfated disaccharide indicating that this saccharide is a repeat of[I_(2S)H_(NS,6S)]. Digestion of the octasulfated hexasaccharide yieldedthe trisulfated disaccharide and a pentasulfated tetrasaccharide. Thatthis tetrasaccharide contains an unsulfated uronic acid was confirmed byheparinase III cleavage, which resulted in the disappearance of thetetrasaccharide. Confirmation of our sequencing assignments were made byisolating the octa- and nonasulfated hexasaccharides and sequenced usingthe methods described herein. Thus, the sequence of the nonasulfatedhexasaccharide is ±DDD (ΔU_(2S)H_(NS,6S)I_(2S)H_(NS,6S)I_(2S)H_(NS,6S))and the sequence of the octasulfated hexasaccharide is ±DD-5.

Saccharide Binding to Antithrombin-III. ATIII is heavily glycosylated,therefore we anticipated that it would not bind well to the MALDI plate.As an alternative strategy, avidin was immobilized on the plate andbiotinylated AT-III was bound to the avidin. The ATIII biotinylationreaction was carried out in the presence of heparin to protect theprotein's binding site for HLGAG oligosaccharides. After washing off thecomplexed heparin, penta 1, that contains an intact AT-IIIpentasaccharide binding sequence was used to verify that the protein wasimmobilized on the surface and was able to bind saccharides. Penta 1binding to ATIII was observed up to washes of 0.5M NaCl, consistent withit being a strong binder to ATIII.

Furthermore, this binding is also specific. Introduction of a solutionof hexa1 , hexa 2, and penta 1 to immobilized ATIII followed by a 0.2 Msalt wash to remove non-specific binders resulted in signal only forpenta 1. Interestingly, there was no signal from hexa 2 that contains apartially intact ATIII binding site, suggesting that, under ourselection conditions, only sequences with a full binding site will beselected for.

Selection of FGF-2 Binders in SMC HS. Heparan sulfate at the cellsurface of SMCs is known to contain high affinity sites for FGF binding.In an effort to extend our initial studies with highly sulfated heparin,we sought to identify high affinity FGF binders in heparan sulfateproteoglycans at the cell surface of SMCs. To this end, SMCs weretreated with either heparinase I or heparinase III and the HLGAGsisolated and purified. Consistent with the known substrate specificityof the enzymes, the composition of released fragments is different.Fragments were then treated with heparinase II to reduce them in size.At certain time points, the digest was spotted on FGF-2 and selectionprocess was accomplished as outlined above. Consistent with our findingswith heparin, a single hexasaccharide was identified to be a highaffinity binder for FGF-2, namely the nonasulfated hexasaccharide with asequence ±DDD.

The above-methodology describes an alternative protocol for theselection of saccharide binders to proteins. This methodology has beenapplied towards the identification of oligosaccharides derived fromheparin that bind to two well-established systems, FGF and ATIII. Asshown, this procedure produces identical results to the more establishedmethodology of affinity fractionation. For FGF-1 and FGF-2, highaffinity binders can be selected out of a pool of similar saccharides.In addition, ATIII, can be selected for high affinity binders overbinders that contain only a partial binding site.

This methodology has a number of critical advantages over prior artstrategies. First, it is possible to derive sequence information fromthe bound saccharides directly on a target. Second, and moresubstantially, the analysis with both FGF and ATIII required onlypicomoles of material for both the protein and saccharide. Such anadvance makes it feasible to use the more biologically relevant HSisolated from the cell surface as substrates, rather than highlysulfated heparin from mast cells. Finally, while the Exampledemonstrated this technique for the chemically complex and informationdense HLGAGs, it is widely applicable towards identifying otherpolysaccharide-protein interactions.

Example 9 Methods for Identifying Branching and Methods for SequencingBranched Polysaccharides

Increasing evidence exists that glycosylation patterns are highlyinfluenced by the phenotype of the cell. With the onset of disease, ithas been noted that there are changes in glycan structure, especially inthe degree of branching. For instance, in pathogenic versus normal prionproteins, there is a decrease in levels of glycans with bisecting GlcNAcresidues and increased levels of tri- and tetrantennary structures. Byjudicious application of enzymatic and chemical degradation the identityof branched chains may also be identified.

MS Analysis of Complex Glycan Structures: As shown in FIG. 8, theextended core structures generated from complex N-glycan structures wereenzymatically generated and identified. MALDI-MS analysis was performedon the extended core structures derived from enzymatic treatment of amixture of bi- and triantennary structures. 1 pmol of each saccharidewas subjected to digest with an enzyme cocktails that included sialidasefrom A. urefaciens and β-galactosidase from S. pneumoniae. The masssignature of 1462.4 indicates that one of the structures is biantennarywith a core fucose moiety, while the mass signature of 1665.8 isindicative of a triantennary structure, also with a core fucose.[◯]=mannose; [●]=fucose; [▪]=N-acetylglucosamine; [□]=galactose; and[Δ]=N-acetylneuraminic acid.

MALDI-MS sequencing of the N-linked polysaccharide of PSA: Next, rapidsequencing of the glycan structure of PSA from normal prostate tissuewas performed (FIG. 9). FIG. 9 is data arising from MALDI-MSmicrosequencing of the PSA polysaccharide structure. MALDI-MS wascompleted using 500 fmol of saccharide. Analysis was completed with asaturated aqueous solution of 2,5-dihydroxybenzoic with 300 mM spermineas an additive. Analytes were detected in the negative mode at anaccelerating voltage of 22 kV. 1 μL of matrix was added to 0.5 μL ofaqueous sample and allowed to dry on the target. (A) MS of the intactpolysaccharide structure. Peaks marked with an asterisk are impurities,and the analyte peak is detected both as M-H (m/z 2369.5) and as amonosodiated adduct (M+Na-2H, m/z 2392.6). (B) Treatment of [A] withsialidase from A. urefaciens. 10 pmol of saccharide was incubated withenzyme overnight at 37° C. in 10 mM sodium acetate pH 5.5 according tothe manufacturer's instructions. Two new saccharides were seen, thefirst, at m/z 2078 corresponding to the loss of one sialic acid moietyand the second at m/z 1786.9 corresponding to the loss of two sialicacids from the non-reducing end. (C) Digest of [B] with galactosidasefrom S. pneumoniae. Digest procedures were completed essentially asdescribed above. A signal product at m/z 1462.8 indicated that twogalactose residues were removed upon treatment of [B] with the enzyme.(D) Digest of [C] with N-acetylhexosaminidase from S. pneumoniae. Oneproduct was observed as both M-H (m/z 1056.3) and M +Na-2H (m/z 1078.1)corresponding to the loss of two N-acetylhexosamine units from [C]. ATable of the analysis scheme with schematic structure and theoreticalmolecular masses is presented in the center of FIG. 9. Shown are theparent polysaccharide and enzymatically derived products seen in thisanalysis. [◯]=mannose; [●]=fucose; [▪]=N-acetylglucosamine;[□]=galactose; and [Δ]=N-acetylneuraminic acid.

Studies of the intact polysaccharide via NMR (large quantities of PSAwere required for this study) yielded sequence information of the glycan[Belanger, A., van Halbeek, H., Graves, H. C. B., Grandbois, K., Stamey,T. A., Huang, L., Poppe, I., and Labrie, F., Prostate, 1995. 27: p.187-197]. Similar to other N-linked glycoproteins, as stated above, PSAcontains a core biantennary branched motif. Extending from each mannosearm of PSA is a trisaccharide unit. Together these modificationsindicated an expected molecular mass of 2370 Da for the intactpolysaccharide. Using MALDI-MS and an exoglycosidase array we havesequenced the putative structure for the N-linked polysaccharide on PSA(FIG. 9). Analysis of the intact polysaccharide yields a molecular massof 2370 Da (FIG. 9A), identical to the predicted molecular mass based onits structure. In fact for all structures and enzymatic products derivedfrom them, a mass accuracy of less than one Dalton is realized.

In initial studies, we had found that maximum sensitivity was obtainedwith 2,5-dihydroxybenzoic acid as the matrix with spermine as anadditive [Mechref, Y. and M. V. Novotny, Matrix-assisted laserdesorption/ionization mass spectrometry of acidic glycoconjugatesfacilitated by the use of spermine as a co-matrix. J Am Soc MassSpectrom, 1998. 9(12): p. 1293-302.]. In this case, oligosaccharideswere detected as negative ions. As outlined above, these conditionsyielded maximal sensitivity (a limit of detection of around 500 fmol orabout 1.5 ng) and also a homogenous signal, which is free of detectableadducts. Of note is the fact that negative mode detection makes amenablethe analysis of sialic-containing pendant arms, but detection can alsobe done in the positive mode with different matrix conditions. Treatmentof the polysaccharide with sialidase (specific cleavage of 2Neuα→6,8linkages) resulted in a mass decrease of 618 Da consistent with thecleavage of two sialic acid residues (FIG. 9B). Treatment of thissaccharide with β-galactosidase resulted in a further 360 Da decrease inmass, confirming the presence of two galactose residues locatedproximate to the sialic acids (FIG. 9C). Importantly when the asilaostructure of FIG. 9B was treated with another enzyme besidesβ-galactosidase, no reduction in mass was observed, confirming theidentity of these units as β-linked galactose residues. Via systematicapplication of the exoglycosidases, we can “read through” the entiresequence of the putative glycan structure of PSA. In addition, not onlycan we “read through” the structure, but our methodology was able tocomplete the analysis using submicrogram amounts of material. Also,since at every step of “reading” the sequence we determined the mass, wehad an internal control to ensure that our assumptions of enzymespecificity and N-glycan structure were correct.

Direct Sequencing of the PSA Polysaccharide Information about thestructure of the sugar moiety of PSA can not only be derived byisolating the sugar and sequencing it (such as by using the abovemethodology), but we can also derive information about the sugarstructure without removal from the protein. FIG. 10 shows the results ofsequencing the sugar of PSA (Sigma Chemical). FIG. 10 shows the resultsof enzymatic degradation of the saccharide chain directly off of PSA. 50pmol of PSA (˜1.4 μg) of PSA was denatured by heat treatment at 80° C.for 20 minutes. Then the sample was sequentially treated with theexoenzymes (B-D). After overnight incubation at 37° C., 1 pmol of thedigested PSA was examined by mass spectrometry. Briefly, the aqueoussample was mixed with sinapinic acid in 30% acetonitrile, allowed todry, and then examined by MALDI TOF. All spectra were calibratedexternally with a mixture of myoglobin, ovalbumin, and BSA to ensureaccurate molecular mass determination. (A) PSA before the addition ofexoenzymes. The measured mass of 28,478 agreed well with the reportedvalue of 28,470. (B) Treatment of (A) with sialidase resulted in a massdecrease of 287 Da, consistent with the loss of one sialic acid residue.(C) Treatment of (B) with galactosidase. A further decrease of 321 Daindicated the loss of two galactose moieties. (D) Upon digestion of (C)with hexosaminidase, a decrease of 393 Da indicated the loss of twoN-acetylglucosamine residues.

The protein had a measured mass of 28,478.3 (FIG. 10A). Treatment of theintact protein with sialidase resulted in a decrease of 287 Da,consistent with the loss of one sialic acid residue (FIG. 10B).Additional treatment with galactosidase resulted in a decrease in massof 321, consistent with the loss of two galactose residues (FIG. 10C).Finally, treatment with N acetylhexosaminidase resulted in cleavage oftwo GlcNAc moieties (FIG. 10D).

Glycotyping of PSA by EndoF2 Treatment EndoF2 is an endoglycanase thatclips only biantennary structures. Tri- and tetrantennary structures donot serve as substrates for this enzyme (FIG. 11). In this way, EndoF2treatment of a glycan structure, either attached to the protein or afterisolation, was used to identify branching identity. This becomesespecially important in light of the fact that aberrant changes inglycosylation patterns usually result in increased branching. Inaddition, EndoF2 was used to cleave glycan structures that were stillattached to the protein of interest. Indeed, treatment of PSA withEndoF2 resulted in mass shift, consistent with the loss of abiantennary, complex type glycan structure. FIG. 11 showed the resultsof treatment of biantennary and triantennary saccharides withendoglycanse F2. (A) Treatment of the biantennary saccharide resulted ina mass decrease of 348.6, indicating cleavage between the GlcNAcresidues. (B) Treatment of the triantennary saccharide with the samesubstituents resulted in no cleavage showing that EndoF2 primarilycleaves biantennary structures. (C) EndoF2 treatment of heat denaturedPSA. There was a mass reduction of 1709.7 Da in the molecular mass ofPSA (compare 11C and 11A) indicating that the normal glycan structure ofPSA was biantennary.

A computer system for implementing the system 100 of FIG. 1 as acomputer program typically includes a main unit connected to both anoutput device which displays information to a user and an input devicewhich receives input from a user. The main unit generally includes aprocessor connected to a memory system via an interconnection mechanism.The input device and output device also are connected to the processorand memory system via the interconnection mechanism.

It should be understood that one or more output devices may be connectedto the computer system. Example output devices include a cathode raytube (CRT) display, liquid crystal displays (LCD), printers,communication devices such as a modem, and audio output. It should alsobe understood that one or more input devices may be connected to thecomputer system. Example input devices include a keyboard, keypad, trackball, mouse, pen and tablet, communication device, and data inputdevices such as sensors. It should be understood the invention is notlimited to the particular input or output devices used in combinationwith the computer system or to those described herein.

The computer system may be a general purpose computer system which isprogrammable using a computer programming language, such as C++, Java,or other language, such as a scripting language or assembly language.The computer system may also include specially programmed, specialpurpose hardware. In a general purpose computer system, the processor istypically a commercially available processor, of which the series x86,Celeron, and Pentium processors, available from Intel, and similardevices from AMD and Cyrix, the 680X0 series microprocessors availablefrom Motorola, the PowerPC microprocessor from IBM and the Alpha-seriesprocessors from Digital Equipment Corporation, are examples. Many otherprocessors are available. Such a microprocessor executes a programcalled an operating system, of which Windows NT, Linux, UNIX, DOS, VMSand OS8 are examples, which controls the execution of other computerprograms and provides scheduling, debugging, input/output control,accounting, compilation, storage assignment, data management and memorymanagement, and communication control and related services. Theprocessor and operating system define a computer platform for whichapplication programs in high-level programming languages are written.

A memory system typically includes a computer readable and writeablenonvolatile recording medium, of which a magnetic disk, a flash memoryand tape are examples. The disk may be removable, known as a floppydisk, or permanent, known as a hard drive. A disk has a number of tracksin which signals are stored, typically in binary form, i.e., a forminterpreted as a sequence of one and zeros. Such signals may define anapplication program to be executed by the microprocessor, or informationstored on the disk to be processed by the application program.Typically, in operation, the processor causes data to be read from thenonvolatile recording medium into an integrated circuit memory element,which is typically a volatile, random access memory such as a dynamicrandom access memory (DRAM) or static memory (SRAM). The integratedcircuit memory element allows for faster access to the information bythe processor than does the disk. The processor generally manipulatesthe data within the integrated circuit memory and then copies the datato the disk after processing is completed. A variety of mechanisms areknown for managing data movement between the disk and the integratedcircuit memory element, and the invention is not limited thereto. Itshould also be understood that the invention is not limited to aparticular memory system.

The invention is not limited to a particular computer platform,particular processor, or particular high-level programming language.Additionally, the computer system may be a multiprocessor computersystem or may include multiple computers connected over a computernetwork. That each module (e.g. 108, 112) in FIG. 1 may be separatemodules of a computer program, or may be separate computer programs.Such modules may be operable on separate computers. Data (e.g. 102, 110,114, 116, and 118) may be stored in a memory system or transmittedbetween computer systems. The invention is not limited to any particularimplementation using software or hardware or firmware, or anycombination thereof. The various elements of the system, eitherindividually or in combination, may be implemented as a computer programproduct tangibly embodied in a machine-readable storage device forexecution by a computer processor. Various steps of the process may beperformed by a computer processor executing a program tangibly embodiedon a computer-readable medium to perform functions by operating on inputand generating output. Computer programming languages suitable forimplementing such a system include procedural programming languages,object-oriented programming languages, and combinations of the two.

The present invention is not to be limited in scope by examplesprovided, since the examples are intended as a single illustration ofone aspect of the invention. Various modifications of the invention inaddition to those shown and described herein will become apparent tothose skilled in the art from the foregoing description and fall withinthe scope of the appended claims. The advantages and objects of theinvention are not necessarily encompassed by each embodiment of theinvention. All references, patents and patent publications that arerecited in this application are incorporated in their entirety herein byreference.

1. In a system including a database of values of properties of polymersof chemical units, a method for determining the composition of a samplepolymer of chemical units having a known molecular length, comprisingsteps of: (A) selecting, from the database, candidate polymers ofchemical units having the same length as the sample polymer of chemicalunits and for which the value of a predetermined property is similar tothe value of the predetermined property of the sample polymer ofchemical units; (B) performing an experiment on the sample polymer ofchemical units; (C) measuring properties of the sample polymer ofchemical units resulting from the experiment; and (D) eliminating, fromthe candidate polymers of chemical units, polymers of chemical unitshaving properties that do not correspond to the experimental results. 2.The method of claim 1, further comprising a step of: (E) repeatedlyperforming the step (D) until the number of candidate polymers ofchemical units falls below a predetermined threshold.
 3. The method ofclaim 1, wherein the predetermined property is molecular weight.
 4. Amethod for identifying a population of polymers of chemical units havingthe same property as a sample polymer of chemical units, comprising:determining a property of a sample polymer of chemical units; comparingthe property of the sample polymer to a reference database of polymersof known sequence and known properties to identify a population ofpolymers of chemical units having the same property as a sample polymerof chemical units, wherein the reference database of polymers includesidentifiers corresponding to the chemical units of the polymers, each ofthe identifiers including a field storing a value corresponding to theproperty.
 5. The method of claim 4, wherein the step of determining aproperty of the sample polymer involves the use of mass spectrometry todetermine the molecular weight of the polymer.
 6. The method of claim 4,wherein the mass spectrometry is MALDI which detects molecular weightwith an accuracy of approximately one Dalton.
 7. The method of claim 4,wherein polymer is reduced to at least two fragments and the property ofthe polymer is the size of the fragments and wherein the step ofdetection involves strong ion exchange chromatography.
 8. The method ofclaim 6, wherein the MALDI analysis is performed on a MALDI surfacehaving a protein coated thereon.
 9. The method of claim 6, wherein thesample polymer is isolated from a cell surface.
 10. A method foridentifying a subpopulation of polymers having a property in common witha sample polymer of chemical units, comprising: (A) applying anexperimental constraint to the polymer to modify the polymer, (B)detecting a property of the modified polymer; (C) identifying apopulation of polymers of chemical units having the same molecularlength as the sample polymer; and (D) identifying a subpopulation of theidentified population of polymers having the same property as themodified polymer by eliminating, from the identified population ofpolymers, polymers having properties that do not correspond to themodified polymer.
 11. The method of claim 10, further comprisingrepeating steps (A), (B), and (D) on the modified polymer to identify asecond subpopulation within the subpopulation of polymers having asecond property in common with the twice modified polymer.
 12. Themethod of claim 11, further comprising repeatedly performing the steps(A), (B), and (D) on the modified polymer until the number of polymerswithin the subpopulation falls below a predetermined threshold.
 13. Themethod of claim 12, wherein the predetermined threshold of polymerswithin the subpopulation is two polymers and wherein the method isperformed to identify the sequence of the polymer.
 14. The method ofclaim 12, wherein the experimental constraints applied to the polymerare different for each repetition. 15-25. (canceled)
 26. A method forcompositional analysis of chemical units of a sample polymer,comprising: (A) applying an experimental constraint to the samplepolymer to modify the sample polymer, (B) detecting a property of themodified sample polymer; (C) comparing the modified sample polymer to areference database of polymers of identical size as the polymer, whereinthe polymers of the reference database have also been subjected to thesame experimental constraint as the sample polymer, wherein thecomparison provides a compositional analysis of the sample polymer.27-29. (canceled)
 30. The method of claim 29, wherein the experimentalconstraint applied to the polymer involves incomplete enzymaticdigestion of the polymer and wherein steps (A), (B), and (C) arerepeated until the number of polymers within the reference databasefalls below a predetermined threshold, and wherein the compositionalanalysis reveals the identity of a sequence of chemical units of thepolymer.
 31. (canceled)
 32. A method for sequencing a polymer,comprising: (A) applying an experimental constraint to the polymer tomodify the polymer, (B) detecting a property of the modified polymer;(C) identifying a population of polymers having the same molecularlength as the sample polymer and having molecular weights similar to themolecular weight of the sample polymer; (D) identifying a subpopulationof the identified population of polymers having the same property as themodified polymer by eliminating, from the identified population ofpolymers, polymers having properties that do not correspond to themodified polymer; (E) repeating steps (A), (B), and (D) by applyingadditional experimental constraints to the polymer and identifyingadditional subpopulations of polymers until the number of polymerswithin the subpopulation is one and the sequence of the polymer may beidentified.
 33. A method for identifying a polysaccharide-proteininteraction, comprising: contacting a protein-coated MALDI surface witha polysaccharide containing sample to produce apolysaccharide-protein-coated MALDI surface, removing unboundpolysaccharide from the polysaccharide-protein-coated MALDI surface, andperforming MALDI mass spectrometry to identify the polysaccharide thatspecifically interacts with the protein coated on the MALDI surface. 34.The method of claim 33, wherein a MALDI matrix is added to thepolysaccharide-protein-coated MALDI surface.
 35. The method of claim 33,further comprising applying an experimental constraint to thepolysaccharide bound on the polysaccharide-protein-coated MALDI surfacebefore performing the MALDI mass spectrometry analysis. 36-38.(canceled)